Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 4 of 25
Found at i:541742 original size:28 final size:28
Alignment explanation
Indices: 541666--542816 Score: 1417
Period size: 28 Copynumber: 40.1 Consensus size: 28
541656 GAACGTTCAT
*
541666 CCCTTTCAAAGCTCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
541694 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
541723 CCCTTTTAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
541751 CTCTTTTCAAAGCTCACGAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
** *
541780 CTTTTTTCAAAGCCCACGAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
541809 TCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
541836 CCCTTTCAAAGCCTACCAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
541864 TCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
541894 CCCTTTAAAAGCCCACGCAAGTTAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
541924 CCCTTTTAAAGCCCACGCAAATCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
541954 CTCTTTTCAAAGCCCACAAGTTAGTGGCT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
541983 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
**
542011 CCCTTTCAAAGCCCATGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542039 CCCTTTCAAAGCCCACGAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542067 CCCTTTTAAAGCCCATGCAAGTTAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
542097 CCCTTTTAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
542127 CTCTTTTCAAAGTCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542156 ACCTTTCAAAGCCCACAAGTCAGTAGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
542184 CCCTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
542212 CCCTTTCAAAGCCCACAAGTCAGTGGGA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
542240 CCCTTTCAAAGCCCACGCAAGTCAATGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
542270 CCCTTTCAAAGCCCACAAGTGAGTGACA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
542298 TCCTTTCAACGCCCACAACTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542326 CCCTTTCAAAGCCCACGAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
542354 CCTTTTCAAAGCCCATC-AGTTAGTCGCA
1 CCCTTTCAAAGCCCA-CAAGTCAGTGGCA
542382 CCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
542412 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542440 CTCTTTCAAAGCCCGCGCAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
542470 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
542498 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
542527 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542555 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
542584 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
542612 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542640 CCCTTTCAAAGCCCAGAAGTGAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542668 CTCTCTTCAAAGCCCACAAGTTAGTGGCA
1 CCCT-TTCAAAGCCCACAAGTCAGTGGCA
* *
542697 TCCTTTCAAAGCCCACAAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
542725 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
542753 CTCTTTCAAAGCCCACACAAGTC-GATGGCAA
1 CCCTTTCAAAG-CC-CACAAGTCAG-TGGC-A
* *
542784 CTCTTTTCAAAGCCCACACAAGTTAGTGGCA
1 C-CCTTTCAAAG-CC-CACAAGTCAGTGGCA
542815 CC
1 CC
542817 ATTTTTTTAA
Statistics
Matches: 987, Mismatches: 111, Indels: 48
0.86 0.10 0.04
Matches are distributed among these distances:
27 26 0.03
28 535 0.54
29 184 0.19
30 191 0.19
31 27 0.03
32 23 0.02
33 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:543447 original size:51 final size:51
Alignment explanation
Indices: 543366--543508 Score: 214
Period size: 51 Copynumber: 2.8 Consensus size: 51
543356 TATGGAAAGG
* *
543366 TACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATTCTTT
1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT
* * * *
543417 TACCTAGATGTATCGATACATTCATCAATGTATCGATATATTCTGTCCTTT
1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT
* *
543468 TACCCGGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACAT
543509 CTAGTTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (51 bp):
TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT
Found at i:545572 original size:27 final size:27
Alignment explanation
Indices: 545534--545605 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
545524 TTTATTTATC
*
545534 GGGGACACTTCAACCCCATTCCTCCGA
1 GGGGATACTTCAACCCCATTCCTCCGA
545561 GGGGATACTTCAACCCCATTCCTCCGA
1 GGGGATACTTCAACCCCATTCCTCCGA
*
545588 GGGGATACTCCAACCCCA
1 GGGGATACTTCAACCCCA
545606 CTTTTAAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.24, C:0.39, G:0.19, T:0.18
Consensus pattern (27 bp):
GGGGATACTTCAACCCCATTCCTCCGA
Found at i:546657 original size:16 final size:16
Alignment explanation
Indices: 546606--546660 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
546596 TGAGTTCGAA
*
546606 TCATTTTAAGTTTAAG
1 TCATTTTAAGTTTAGG
* * * *
546622 TTATTCTAAATTTTGG
1 TCATTTTAAGTTTAGG
546638 TCATTTTAAGTTTAGG
1 TCATTTTAAGTTTAGG
546654 TCATTTT
1 TCATTTT
546661 CGGGTTTAGA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.55
Consensus pattern (16 bp):
TCATTTTAAGTTTAGG
Found at i:548189 original size:13 final size:13
Alignment explanation
Indices: 548168--548198 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
548158 CAATACATGG
*
548168 TACAATGTATCGA
1 TACATTGTATCGA
548181 TACATTGTATCGA
1 TACATTGTATCGA
548194 TACAT
1 TACAT
548199 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:548199 original size:76 final size:76
Alignment explanation
Indices: 548108--548349 Score: 247
Period size: 76 Copynumber: 3.2 Consensus size: 76
548098 TACATGGACA
548108 ATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTACAA
1 ATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTACAA
548173 TGTATCGATAC
66 TGTATCGATAC
** * * * *
548184 ATTGTATCGATACATGATGAATT----GTA--T-CAATA-CATTGCTTGTA-ACGGCTATAAATG
1 ATTGTATCGATACATGA--AATTGGCAGTAGCTACCCTACCACTG-TT-TATA--TCAATACATG
* *
548240 GCTATAAT-T-TC-AAATC
60 G-TACAATGTATCGATA-C
548256 AATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTACA
1 -ATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTACA
548321 ATGTATCGATAC
65 ATGTATCGATAC
548333 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
548350 TGAATTGTAT
Statistics
Matches: 129, Mismatches: 16, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
70 4 0.03
71 12 0.09
72 6 0.05
73 26 0.20
74 8 0.06
75 8 0.06
76 43 0.33
77 6 0.05
78 12 0.09
79 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (76 bp):
ATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTACAA
TGTATCGATAC
Found at i:548338 original size:13 final size:13
Alignment explanation
Indices: 548317--548347 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
548307 CAATACATGG
*
548317 TACAATGTATCGA
1 TACATTGTATCGA
548330 TACATTGTATCGA
1 TACATTGTATCGA
548343 TACAT
1 TACAT
548348 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:548376 original size:149 final size:149
Alignment explanation
Indices: 548106--548419 Score: 621
Period size: 149 Copynumber: 2.1 Consensus size: 149
548096 GATACATGGA
548106 CAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTAC
1 CAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTAC
548171 AATGTATCGATACATTGTATCGATACATGATGAATTGTATCAATACATTGCTTGTAACGGCTATA
66 AATGTATCGATACATTGTATCGATACATGATGAATTGTATCAATACATTGCTTGTAACGGCTATA
548236 AATGGCTATAATTTCAAAT
131 AATGGCTATAATTTCAAAT
548255 CAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTAC
1 CAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTAC
548320 AATGTATCGATACATTGTATCGATACATGATGAATTGTATCAATACATTGCTTGTAACGGCTATA
66 AATGTATCGATACATTGTATCGATACATGATGAATTGTATCAATACATTGCTTGTAACGGCTATA
548385 AATGGCTATAATTTCAAAT
131 AATGGCTATAATTTCAAAT
548404 CAA-TGTATCGATACAT
1 CAATTGTATCGATACAT
548420 TATGAATTGT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 13 0.08
149 152 0.92
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (149 bp):
CAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTACCACTGTTTATATCAATACATGGTAC
AATGTATCGATACATTGTATCGATACATGATGAATTGTATCAATACATTGCTTGTAACGGCTATA
AATGGCTATAATTTCAAAT
Found at i:553552 original size:3 final size:3
Alignment explanation
Indices: 553544--553587 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
553534 AATAACTCTT
553544 TTA TTA 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
553588 TTTTGATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:554494 original size:25 final size:24
Alignment explanation
Indices: 554437--554495 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
554427 AATTGGCTAC
* * *
554437 AAAACAACAAAGAAAAAAATCACG
1 AAAACAAAAAAAAAAAAAATCAAG
*
554461 AAAAAAAAAAAAAAAAAAACTCAAG
1 AAAACAAAAAAAAAAAAAA-TCAAG
*
554486 CAAACAAAAA
1 AAAACAAAAA
554496 TTACTTGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.78, C:0.14, G:0.05, T:0.03
Consensus pattern (24 bp):
AAAACAAAAAAAAAAAAAATCAAG
Found at i:554852 original size:35 final size:35
Alignment explanation
Indices: 554813--554886 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
554803 CTTAACATAT
554813 ATATATAAAATTTATTTTTAATATCTAATCAAAAC
1 ATATATAAAATTTATTTTTAATATCTAATCAAAAC
* *
554848 ATATATAAAATTTATTTTTAATATTTAATCAAAAT
1 ATATATAAAATTTATTTTTAATATCTAATCAAAAC
554883 ATAT
1 ATAT
554887 TAATAAGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (35 bp):
ATATATAAAATTTATTTTTAATATCTAATCAAAAC
Found at i:554983 original size:29 final size:29
Alignment explanation
Indices: 554941--555008 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
554931 TAAAATTACT
554941 TAATAAAATAATATAACTTAATTTATTAA
1 TAATAAAATAATATAACTTAATTTATTAA
554970 TAATAAAATAATATAACTTAATTTATTAA
1 TAATAAAATAATATAACTTAATTTATTAA
554999 TAATATAAAT
1 TAATA-AAAT
555009 TAAATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATAAAATAATATAACTTAATTTATTAA
Found at i:555068 original size:27 final size:28
Alignment explanation
Indices: 555031--555095 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
555021 AAAATTCACT
555031 ACTTAGATAAAAACTTAACATTAAA-TTA
1 ACTTAG-TAAAAACTTAACATTAAATTTA
**
555059 ACTTAGT-AAAACTTAATTTTAAATTTA
1 ACTTAGTAAAAACTTAACATTAAATTTA
*
555086 ACTTATTAAA
1 ACTTAGTAAA
555096 TTTTAATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 14 0.44
27 10 0.31
28 8 0.25
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (28 bp):
ACTTAGTAAAAACTTAACATTAAATTTA
Found at i:555096 original size:14 final size:14
Alignment explanation
Indices: 555050--555098 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
555040 AAAACTTAAC
555050 ATTAAA-TTAACTT
1 ATTAAATTTAACTT
* *
555063 AGTAAAACTTAA-TT
1 A-TTAAATTTAACTT
555077 -TTAAATTTAACTT
1 ATTAAATTTAACTT
555090 ATTAAATTT
1 ATTAAATTT
555099 TAATAACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 14 0.48
15 4 0.14
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTAAATTTAACTT
Found at i:555943 original size:29 final size:31
Alignment explanation
Indices: 555891--555949 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
555881 TTAGGAGAAA
555891 AATAATATTCTTTTCAAATATAATA-ATATC
1 AATAATATTCTTTTCAAATATAATATATATC
555921 AATAATA-TCTTTT-AAATATTAATATATAT
1 AATAATATTCTTTTCAAATA-TAATATATAT
555950 TATAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (31 bp):
AATAATATTCTTTTCAAATATAATATATATC
Found at i:556988 original size:20 final size:22
Alignment explanation
Indices: 556963--557010 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 22
556953 ATCGCCAAGC
556963 AAATTAAAAAAAAATTA-ATT-
1 AAATTAAAAAAAAATTATATTG
556983 AAATT-AAAAAAAATTATATTG
1 AAATTAAAAAAAAATTATATTG
557004 AAATTAA
1 AAATTAA
557011 TGTATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.44
20 8 0.32
21 5 0.20
22 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAAAAAAAAATTATATTG
Found at i:557069 original size:21 final size:22
Alignment explanation
Indices: 557027--557079 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
557017 AATTATTAAT
557027 TTTTAA-TAAAATAAAAATAAA
1 TTTTAATTAAAATAAAAATAAA
* *
557048 TTTTAATTAAATTTAAAA-AAA
1 TTTTAATTAAAATAAAAATAAA
*
557069 TTGT-ATTAAAA
1 TTTTAATTAAAA
557080 AATTAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTAATTAAAATAAAAATAAA
Found at i:557117 original size:68 final size:70
Alignment explanation
Indices: 556977--557127 Score: 177
Period size: 73 Copynumber: 2.1 Consensus size: 70
556967 TAAAAAAAAA
*
556977 TTAATTAAATTAAAAAAAATTATATTGAAATTAATGTATTAATTATTAATTTTTAATAAAATAAA
1 TTAATTAAATTAAAAAAAATTATATTAAAATTAATGTATTAATTATTAATTTTT-AT-AAAT-AA
557042 AATAAATT
63 AATAAATT
* *
557050 TTAATTAAATTTAAAAAAATTGTATTAAAAAATTAAAT-TATTAATTATTAATTTTT-T-AAT-A
1 TTAATTAAATTAAAAAAAATTATATT--AAAATT-AATGTATTAATTATTAATTTTTATAAATAA
557111 AA-AAATT
63 AATAAATT
557118 TTAAATTAAA
1 TT-AATTAAA
557128 AAAATTAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
68 7 0.10
69 10 0.14
71 3 0.04
73 25 0.35
75 23 0.32
76 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (70 bp):
TTAATTAAATTAAAAAAAATTATATTAAAATTAATGTATTAATTATTAATTTTTATAAATAAAAT
AAATT
Found at i:557473 original size:23 final size:22
Alignment explanation
Indices: 557424--557473 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
557414 AGGTAATTTA
*
557424 AATTTATTTTATTTTAAGGTAT
1 AATTTATTTTATTTTAAGATAT
*
557446 GATTTATTTTTATTTGTAAGAT-T
1 AATTTA-TTTTATTT-TAAGATAT
557469 AATTT
1 AATTT
557474 GATTATAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 5 0.22
23 13 0.57
24 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (22 bp):
AATTTATTTTATTTTAAGATAT
Found at i:557647 original size:76 final size:73
Alignment explanation
Indices: 557481--557698 Score: 225
Period size: 76 Copynumber: 3.0 Consensus size: 73
557471 TTTGATTATA
* * * *
557481 AGTATTATTCATTTTTATTTTTAGAAGTTTAAATTTA-TTTTTA-TTTGA-T-TATGAGGATTTA
1 AGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTTTTAGTTTGATTATATGA-GATTTA
557542 AATTTTTAG
65 AATTTTTAG
* * * *
557551 AGTATAATTTGTTTTGATTTGTAGAAATTTAAATTTATTATTTTAGGTATGATTATATGAGTTTT
1 AGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATT-TTTTA-GTTTGATTATATGAGATTT
557616 AAATTTTT-G
64 AAATTTTTAG
* * *
557625 ATGTTGTAATTTATTTTTATTTGTAAAAATTTAAAATTTATTTTTT-GATTTGATTATAT-AAAT
1 A-G-TATAATTTATTTTTATTTGTAGAAATTT-AAATTTATTTTTTAG-TTTGATTATATGAGAT
557688 TTAAATTTTTA
62 TTAAATTTTTA
557699 AGCGTAGTGG
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
70 31 0.25
71 1 0.01
72 5 0.04
74 19 0.16
75 24 0.20
76 33 0.27
77 9 0.07
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (73 bp):
AGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTTTTAGTTTGATTATATGAGATTTAA
ATTTTTAG
Found at i:557794 original size:11 final size:12
Alignment explanation
Indices: 557768--557822 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
557758 GGGAGGAGTG
*
557768 AAGAAGAAAGGA
1 AAGAAGAAAAGA
557780 AAGAA-AAAAGA
1 AAGAAGAAAAGA
**
557791 AAGAAGGGAAG-
1 AAGAAGAAAAGA
*
557802 AAGAAAAAAAG-
1 AAGAAGAAAAGA
557813 AAGAAGAAAA
1 AAGAAGAAAA
557823 AGGAAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
11 27 0.77
12 8 0.23
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGA
Found at i:557797 original size:19 final size:18
Alignment explanation
Indices: 557775--557828 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
557765 GTGAAGAAGA
557775 AAGGAAAGAAAAAAGAAAG
1 AAGG-AAGAAAAAAGAAAG
557794 AAGGGAAGAAGAAAA-AAAG
1 AA-GGAAGAA-AAAAGAAAG
*
557813 AA-GAAGAAAAAGGAAA
1 AAGGAAGAAAAAAGAAA
557829 AATAAAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.10
17 9 0.29
19 13 0.42
20 6 0.19
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAGGAAGAAAAAAGAAAG
Found at i:558470 original size:157 final size:157
Alignment explanation
Indices: 558098--558540 Score: 533
Period size: 157 Copynumber: 2.8 Consensus size: 157
558088 AAGTTTAATG
*
558098 TAGTTTTA-GTTATATTTTTTATTTAATATGAAATACTCGTTTAAATATCTTTTGATGTTATTTA
1 TAGTTTTAGGTTATA-TTTTTATTTAATATGAAATACTCGTTTAAATATC-TTTGATGTTATTTG
* * * *
558162 AGATTTTTGATATTATTAA-TTTTTTATGACATACTTGTTTAATATGTTAGAATATTTTTAA-CA
64 AGATTTTTGATATTATTAATTTTTTTATGACATGCTTGTTTAATATG-TAAAATATGTTTAATAA
* * *
558225 TGTCAAAAATAAAAAAGATTTAGTTTGACG
128 TGTCAAAAATAAAAAAGACTTAGATTGACA
* * * * * * *
558255 T-GATTTTGGGTGATAAATTTTATTTAATATGAACTCCTCGTTTAGATACCTTTAGATGTTATTT
1 TAG-TTTTAGGTTAT-ATTTTTATTTAATATGAAATACTCGTTTAAATATCTTT-GATGTTATTT
* * *
558319 GAGATTTCTAATATTATTAATTTTTTTATTG-CATGCTTATTTAATATGTCAAAATATGTTTAAT
63 GAGATTTTTGATATTATTAATTTTTTTA-TGACATGCTTGTTTAATATGT-AAAATATGTTTAAT
558383 AAT-T-AAAAAT-AAAAAGACTTAGATTGACA
126 AATGTCAAAAATAAAAAAGACTTAGATTGACA
* *
558412 TAGTTTTAGGTTATATTTGTTATTTAATATGAAATGCTCGTTTAAATATCTCTTGATGTTGTTTG
1 TAGTTTTAGGTTATATTT-TTATTTAATATGAAATACTCGTTTAAATATCT-TTGATGTTATTTG
* *
558477 ATATTTTTGATATTATTAATTTTTTTATGATATGCTTGTTTAATATGGTAAAATATGTTTAATA
64 AGATTTTTGATATTATTAATTTTTTTATGACATGCTTGTTTAATAT-GTAAAATATGTTTAATA
558541 TCATTAATTT
Statistics
Matches: 242, Mismatches: 31, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
156 6 0.02
157 125 0.52
158 72 0.30
159 35 0.14
160 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (157 bp):
TAGTTTTAGGTTATATTTTTATTTAATATGAAATACTCGTTTAAATATCTTTGATGTTATTTGAG
ATTTTTGATATTATTAATTTTTTTATGACATGCTTGTTTAATATGTAAAATATGTTTAATAATGT
CAAAAATAAAAAAGACTTAGATTGACA
Found at i:560017 original size:19 final size:21
Alignment explanation
Indices: 559971--560024 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
559961 TTTCAATAAT
559971 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
559992 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
560011 TTGTATCGATACAA
1 TTGTATCGATACAA
560025 TGTATCGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:560030 original size:13 final size:13
Alignment explanation
Indices: 560012--560036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560002 ACATAAGTAT
560012 TGTATCGATACAA
1 TGTATCGATACAA
560025 TGTATCGATACA
1 TGTATCGATACA
560037 TAACTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:560032 original size:32 final size:32
Alignment explanation
Indices: 559991--560068 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
559981 ACAAACAGTA
*
559991 AATGTATCGATACATAAGTATTGTATCGATAC
1 AATGTATCGATACATAACTATTGTATCGATAC
* *
560023 AATGTATCGATACATAACTGTTGTATCTATAC
1 AATGTATCGATACATAACTATTGTATCGATAC
*
560055 AATGTATCGCTACA
1 AATGTATCGATACA
560069 ACGCTACTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAACTATTGTATCGATAC
Found at i:560049 original size:19 final size:18
Alignment explanation
Indices: 559971--560056 Score: 56
Period size: 19 Copynumber: 4.8 Consensus size: 18
559961 TTTCAATAAT
*
559971 TTGTATCGATACAAACAG
1 TTGTATCGATACAAACTG
* *
559989 TAAATGTATCGATACATAAGTA
1 T---TGTATCGATACA-AACTG
560011 TTGTATCGATAC-AA---
1 TTGTATCGATACAAACTG
560025 -TGTATCGATACATAACTG
1 TTGTATCGATACA-AACTG
*
560043 TTGTATCTATACAA
1 TTGTATCGATACAA
560057 TGTATCGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
18 2 0.04
19 22 0.41
21 12 0.22
22 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAAACTG
Found at i:560105 original size:13 final size:13
Alignment explanation
Indices: 560087--560113 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
560077 GCTAAGGAAA
560087 TGTATCGATACAT
1 TGTATCGATACAT
560100 TGTATCGATACAT
1 TGTATCGATACAT
560113 T
1 T
560114 AATCTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:566904 original size:52 final size:52
Alignment explanation
Indices: 566848--566976 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
566838 CACTGATCTT
*
566848 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
566900 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATTTAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
566952 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
566977 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:573174 original size:31 final size:30
Alignment explanation
Indices: 573136--573250 Score: 142
Period size: 30 Copynumber: 3.7 Consensus size: 30
573126 ATACCTTTTT
*
573136 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
*
573167 AAAGTCCAAGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCTC
*
573197 AAAGTCCACGACTTAGTGGCATCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAT-CTTTTC-TC
* *
573229 AAAGCCCACGAATCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
573251 TTTGTTTTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.03
30 26 0.36
31 21 0.29
32 24 0.33
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTC
Found at i:573254 original size:62 final size:61
Alignment explanation
Indices: 573136--573255 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 61
573126 ATACCTTTTT
* *
573136 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCAAGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCAAGAATCAGTGGCATTTTGTCTC
* * *
573197 AAAGTCCACGACTTAGTGGC-ATCCTTTTCTTCAAAGCCCACGAATCAGTGGCATTTTGT
1 AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TCAAAGCCCAAGAATCAGTGGCATTTTGT
573256 TTTAAAGCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 2 0.04
61 24 0.46
62 26 0.50
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCAAGAATCAGTGGCATTTTGTCTC
Found at i:573265 original size:30 final size:30
Alignment explanation
Indices: 573136--573267 Score: 131
Period size: 30 Copynumber: 4.3 Consensus size: 30
573126 ATACCTTTTT
* * *
573136 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCATTTTGTT-TC
* *
573167 AAAGTCCAAGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTTTGTTTC
*
573197 AAAGTCCACGACTTAGTGGCATCCTTT-TCTTC
1 AAAGTCCACGACTCAGTGGCAT--TTTGT-TTC
* * *
573229 AAAGCCCACGAATCAGTGGCATTTTGTTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTTTC
*
573259 AAAGCCCAC
1 AAAGTCCAC
573268 AATTTCGTGG
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
30 36 0.42
31 25 0.29
32 24 0.28
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATTTTGTTTC
Found at i:573305 original size:35 final size:33
Alignment explanation
Indices: 573256--573538 Score: 150
Period size: 33 Copynumber: 8.7 Consensus size: 33
573246 GGCATTTTGT
* *
573256 TTTAAAGCCCACAATT-TCGTGGGAACTTTTTTC
1 TTTAAAGCCCACAATTCT-GTGGCAACTTTTTCC
*
573289 TTCTCAAAGCCCACAATTCTGTGGCACCTTTTTCC
1 TT-T-AAAGCCCACAATTCTGTGGCAACTTTTTCC
*
573324 TTTAAAGCCCACAACTAC-GTGGC-ACTCTTTTCC
1 TTTAAAGCCCACAA-TTCTGTGGCAACT-TTTTCC
* * * *
573357 TTTTAAGTCCACAACTCTGTGGC-AC-----CA
1 TTTAAAGCCCACAATTCTGTGGCAACTTTTTCC
* * * *
573384 TTTTAAGCCCACAACTCCGTGGCATCTTTTTCC
1 TTTAAAGCCCACAATTCTGTGGCAACTTTTTCC
* *
573417 TTTTCAAAGCCCACAACTCCGTGGC-AC-----CC
1 -TTT-AAAGCCCACAATTCTGTGGCAACTTTTTCC
* * * *
573446 TTTTAAGCCCACAACTCCGTGGCACCCTCTTTTTCC
1 TTTAAAGCCCACAATTCTGTGGCA---ACTTTTTCC
*
573482 TTTAAAGCCCACAACTAC-GTGGC-ACTCTTTTCC
1 TTTAAAGCCCACAA-TTCTGTGGCAACT-TTTTCC
* *
573515 TTTTAAGTCCACAATTCTGTGGCA
1 TTTAAAGCCCACAATTCTGTGGCA
573539 CCATTTTAAG
Statistics
Matches: 198, Mismatches: 25, Indels: 53
0.72 0.09 0.19
Matches are distributed among these distances:
27 41 0.21
28 4 0.02
29 2 0.01
31 1 0.01
32 7 0.04
33 67 0.34
34 8 0.04
35 46 0.23
36 21 0.11
37 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (33 bp):
TTTAAAGCCCACAATTCTGTGGCAACTTTTTCC
Found at i:573395 original size:27 final size:27
Alignment explanation
Indices: 573355--573878 Score: 301
Period size: 27 Copynumber: 17.2 Consensus size: 27
573345 GCACTCTTTT
* *
573355 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
573382 CATTTTAAGCCCACAACTCCGTGGCATC
1 CCTTTTAAGCCCACAACTCCGTGGCA-C
573410 TTTTTCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 -----CCTTTT--AAGCCCACAACTCCGTGGCAC
573444 CCTTTTAAGCCCACAACTCCGTGGCACC
1 CCTTTTAAGCCCACAACTCCGTGGCA-C
*
573472 CTCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTC
1 C-C----T--TTT-AAGCCCACAACTCCGTGGCA--C
* * *
573509 TTTTCCTTTTAAGTCCACAATTCTGTGGCAC
1 ----CCTTTTAAGCCCACAACTCCGTGGCAC
* *
573540 CATTTTAAGCCCACAACTTCGTGGCATC
1 CCTTTTAAGCCCACAACTCCGTGGCA-C
* *
573568 TTTTTCCTTTTAAGTCCACGACTCCGTGGCAC
1 -----CCTTTTAAGCCCACAACTCCGTGGCAC
* *
573600 TCTTTTTAAAGCCCATAACTCCGTGGCAC
1 -CCTTTT-AAGCCCACAACTCCGTGGCAC
* *
573629 CCTTTTAAGTCCACGACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
573656 CCTTTTTTCCTTTAAAGCCCACAACTCCGTGGCAC
1 CC-----T--TTT-AAGCCCACAACTCCGTGGCAC
*
573691 CCGTTTAAGCCCACAACTCCGTGGCACTC
1 CCTTTTAAGCCCACAACTCCGTGGCA--C
*
573720 TTTTTCCTTCTAAGCCCACAACTCCGTGGCAC
1 -----CCTTTTAAGCCCACAACTCCGTGGCAC
573752 CTTCTTTTCAAAGCCCACAACTCCGTGGCACCC
1 C--CTTTT--AAGCCCACAACTCCGTGGCA--C
* *
573785 TTTTTCCTTTTAAGTCCACGACTCCGTGGCAC
1 -----CCTTTTAAGCCCACAACTCCGTGGCAC
*
573817 TCTTTTTAAAGCCCACAACTCCGTGGCAC
1 -CCTTTT-AAGCCCACAACTCCGTGGCAC
** *
573846 CCTTTTAAGTGCACGACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
573873 TCTTTT
1 CCTTTT
573879 TCTTTTTAAG
Statistics
Matches: 398, Mismatches: 43, Indels: 112
0.72 0.08 0.20
Matches are distributed among these distances:
27 128 0.32
28 29 0.07
29 49 0.12
31 21 0.05
32 4 0.01
33 45 0.11
34 49 0.12
35 44 0.11
36 25 0.06
37 1 0.00
38 1 0.00
40 1 0.00
41 1 0.00
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:573457 original size:62 final size:61
Alignment explanation
Indices: 573322--573851 Score: 475
Period size: 62 Copynumber: 8.5 Consensus size: 61
573312 GCACCTTTTT
* * * *
573322 CCTTTAAAGCCCACAACTACGTGGCA-CTCTTTTCCTTTT-AAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCACCT-TTTTCCTTTTAAAGCCCACAACTCCGTGGCAC
* *
573382 CATTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCAC
*
573444 CCTTTTAAGCCCACAACTCCGTGGCACCCTCTTTTTCC-TTTAAAGCCCACAACTACGTGGCACT
1 CCTTTTAAGCCCACAACTCCGTGGCA--C-CTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA--
573508 C
61 C
* * * * *
573509 TTTTCCTTTTAAGTCCACAATTCTGTGGCA-C-----CATTTT-AAGCCCACAACTTCGTGGCAT
1 ----CCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA-
573567 C
61 C
* * * *
573568 TTTTTCCTTTTAAGTCCACGACTCCGTGGCA-C----TCTTTTTAAAGCCCATAACTCCGTGGCA
1 -----CCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA
573628 C
61 C
* *
573629 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTTCC-TTTAAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCA-CC-TTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC
* *
573691 CCGTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC
* *
573752 CTTCTTTTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT-AAGTCCACGACTCCGTGGCA
1 C--CTTTT--AAGCCCACAACTCCGTGGCA-CCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA
573816 C
61 C
* *
573817 TCTTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
1 -CCTTTT-AAGCCCACAACTCCGTGGCACCTTTTT
573852 AAGTGCACGA
Statistics
Matches: 408, Mismatches: 31, Indels: 60
0.82 0.06 0.12
Matches are distributed among these distances:
56 26 0.06
58 1 0.00
59 2 0.00
60 81 0.20
61 41 0.10
62 118 0.29
63 47 0.12
64 7 0.02
65 60 0.15
66 2 0.00
69 23 0.06
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.31
Consensus pattern (61 bp):
CCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC
Found at i:573491 original size:158 final size:157
Alignment explanation
Indices: 573294--573905 Score: 729
Period size: 158 Copynumber: 4.0 Consensus size: 157
573284 TTTTCTTCTC
* *
573294 AAAGCCCACAATTCTGTGGCA-CCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCT
1 AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCT
* * *
573358 TTTAAGTCCACAACTCTGTGGCACCATTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTTTC
66 TTAAAGCCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT-
*
573422 AAAGCCCACAACTCCGTGGCACCCTTTT
130 TAAGCCCACAACTCCGTGGCACCCTTTT
573450 -AAGCCCACAACTCCGTGGCACCCTCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTC
1 AAAGCCCACAACTCCGTGGCA-CC-CTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTC
* * * * *
573514 CTTTTAAGTCCACAATTCTGTGGCACCATTTTAAGCCCACAACTTCGTGGCA-TCTTTTTCC-TT
64 CTTTAAAGCCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* * *
573577 TTAAGTCCACGACTCCGTGGCACTCTTTTT
129 TTAAGCCCACAACTCCGTGGCAC-CCTTTT
* * * * *
573607 AAAGCCCATAACTCCGTGGCACCC----T--TTT-AAGTCCACGACTCCGTGGCACCCTTTTTTC
1 AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTAAAGCCCACAACTACGTGGCA--CTCTTTTC
**
573665 CTTTAAAGCCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTCTTTTTCC-TT
64 CTTTAAAGCCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
*
573729 CTAAGCCCACAACTCCGTGGCACCTTCTTTT
129 TTAAGCCCACAACTCCGTGGCACC--CTTTT
* * * *
573760 CAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACGACTCCGTGGCACTC--TT--
1 -AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCC
* ** *
573821 TTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTGCACGACTCCGTGGCACTCTTTTT-CTTTT
65 TTTAAAGCCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
573885 TAAGCCCACAAGTCAGTGGCA
130 TAAGCCCACAACTCCGTGGCA
573906 TTTTTTTTCA
Statistics
Matches: 404, Mismatches: 33, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
149 17 0.04
150 3 0.01
151 53 0.13
152 32 0.08
153 4 0.01
154 24 0.06
155 94 0.23
156 20 0.05
157 13 0.03
158 119 0.29
159 2 0.00
160 3 0.01
161 20 0.05
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (157 bp):
AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCT
TTAAAGCCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTT
AAGCCCACAACTCCGTGGCACCCTTTT
Found at i:573563 original size:60 final size:62
Alignment explanation
Indices: 573482--573655 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 62
573472 CTCTTTTTCC
* *
573482 TTTAAAGCCCACAACTACGTGGCACTCTTTTCCTTTTAAGTCCACAATTCTGTGGCAC-CAT
1 TTTAAAGCCCACAACTACGTGGCACTCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCAT
* * *
573543 TTT-AAGCCCACAACTTCGTGGCA-TCTTTTTCCTTTTAAGTCCACGACTCCGTGGCACTCTT
1 TTTAAAGCCCACAACTACGTGGCACTC-TTTTCCTTTTAAGTCCACAACTCCGTGGCACTCAT
* * *
573604 TTTAAAGCCCATAACTCCGTGGCA--C----CCTTTTAAGTCCACGACTCCGTGGCAC
1 TTTAAAGCCCACAACTACGTGGCACTCTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
573656 CCTTTTTTCC
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
56 27 0.26
59 2 0.02
60 47 0.46
61 9 0.09
62 18 0.17
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.32
Consensus pattern (62 bp):
TTTAAAGCCCACAACTACGTGGCACTCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCAT
Found at i:573701 original size:89 final size:90
Alignment explanation
Indices: 573388--573851 Score: 431
Period size: 96 Copynumber: 4.9 Consensus size: 90
573378 GCACCATTTT
573388 AAGCCCACAACTCCGTGGCATCTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAG
1 AAGCCCACAACTCCGTGGCA-C----TCCTTTT--AAGCCCACAACTCCGTGGCACCCTTTTAAG
573453 CCCACAACTCCGTGGCACCCTCTTTTTCCTTTA
59 CCCACAACTCCGTGGCACCCT-TTTTTCCTTTA
* * * * *
573486 AAGCCCACAACTACGTGGCACTCTTTTCCTTTTAAGTCCACAATTCTGTGGCACCATTTTAAGCC
1 AAGCCCACAACTCCGTGGCA--C---TCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTAAGCC
* * *
573551 CACAACTTCGTGGCA-TC-TTTTTCCTTTT
61 CACAACTCCGTGGCACCCTTTTTTCCTTTA
* * * * * *
573579 AAGTCCACGACTCCGTGGCACTCTTTTTAAAGCCCATAACTCCGTGGCACCCTTTTAAGTCCACG
1 AAGCCCACAACTCCGTGGCACTCCTTTT-AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACA
573644 ACTCCGTGGCACCCTTTTTTCCTTTA
65 ACTCCGTGGCACCCTTTTTTCCTTTA
* *
573670 AAGCCCACAACTCCGTGGCAC-CCGTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAG
1 AAGCCCACAACTCCGTGGCACTCCTTTTAAGCCCACAACTCCGTGGCA--C-----CCTTTTAAG
573734 CCCACAACTCCGTGGCA-CCTTCTTTT-C---A
59 CCCACAACTCCGTGGCACCCTT-TTTTCCTTTA
* * *
573762 AAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACGACTCCGTGGCACTCTTTTTAAA
1 AAGCCCACAACTCCGTGGCA--C----TCCTTTTAAGCCCACAACTCCGTGGCAC-CCTTTT-AA
573827 GCCCACAACTCCGTGGCACCCTTTT
58 GCCCACAACTCCGTGGCACCCTTTT
573852 AAGTGCACGA
Statistics
Matches: 310, Mismatches: 35, Indels: 46
0.79 0.09 0.12
Matches are distributed among these distances:
88 6 0.02
89 58 0.19
90 5 0.02
91 31 0.10
92 21 0.07
93 32 0.10
94 23 0.07
95 10 0.03
96 69 0.22
97 1 0.00
98 29 0.09
99 25 0.08
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.30
Consensus pattern (90 bp):
AAGCCCACAACTCCGTGGCACTCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAA
CTCCGTGGCACCCTTTTTTCCTTTA
Found at i:573922 original size:247 final size:243
Alignment explanation
Indices: 573295--574137 Score: 636
Period size: 247 Copynumber: 3.4 Consensus size: 243
573285 TTTCTTCTCA
* * * * *
573295 AAGCCCACAATTCTGTGGCACCTTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCTTT
1 AAGCCCACAACTCCGTGGCATCTTCTT-CTTTAAAGCCCACAACTCCGTGGCA--C---TCCTTT
* * *
573360 T-AAGTCCACAACTCTGTGGCACCATTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTCAA
60 TAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-C-TTTT--TTTTCAA
573424 AGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTCTTTTTCCTT-TAAA
121 AGCCCACAACTCCGTGGCACCC-TTTAAGCCCACAACTCCGTGGCA--CTCTTTTTCCTTCT-AA
* * * *
573488 GCCCACAACTACGTGGCACTCTTTTCCTTTT--AAGTCCACAATTCTGTGGCA-C-----CATTT
182 GCCCACAACTCCGTGGCAC-C--TT-CTTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
573545 T
243 T
* * * * * *
573546 AAGCCCACAACTTCGTGGCATCTTTTTCCTTTTAAGTCCACGACTCCGTGGCACTCTTTTTAAAG
1 AAGCCCACAACTCCGTGGCATCTTCTT-CTTTAAAGCCCACAACTCCGTGGCACTCCTTTTAAAG
* * * *
573611 CCCATAACTCCGTGGCACCCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTTCCTTTAAAGCCC
65 CCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA--CTTTTTT--TTCAAAGCCC
573676 ACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAA
126 ACAACTCCGTGGCACCC-TTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAA
*
573741 CTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT
190 CTCCGTGGCACCTTCTTTTCAAAGTCCACAACTCCGTGGCA-CCTTTTTCCTTTT
* * *
573796 AAGTCCACGACTCCGTGGCA-C-TCTT-TTTAAAGCCCACAACTCCGTGGCAC-CCTTTT-AAGT
1 AAGCCCACAACTCCGTGGCATCTTCTTCTTTAAAGCCCACAACTCCGTGGCACTCCTTTTAAAGC
* * * *
573856 GCACGACTCCGTGGCACTCTTTTTCTTTTTAAGCCCACAAGTCAGTGGCA-TTTTTTTTCAAAAG
66 CCACAACTCCGTGGCAC-C-----C-TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTC-AAAG
* * * * * * * *
573920 CCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCAC-CCTTTT-C--CGAAGCCCA
123 CCCACAACTCCGTGGCACCCTT-TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCA
* * *
573981 CAAGTCGGTGGCA---TCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGT
187 CAACTCCGTGGCACCTTCTTTT-CAAAGTCCACAACTCCGTGGCAC-CTTTTTCCTTT-T
** ** * * * * ** *
574038 AAGCTTACAACTCTATAGCACTCTTTTTCTTTTTAAGCCCACAAGTTAGCGGCAC-CCTTTTCAA
1 AAGCCCACAACTCCGTGGCA-TCTTCTTC-TTTAAAGCCCACAACTCCGTGGCACTCCTTTT--A
* * * * *
574102 AAGCCCACAAGTCAGTGGCAACCTCTAAAGCCCACA
62 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACA
574138 CAAGTTGGTG
Statistics
Matches: 485, Mismatches: 73, Indels: 76
0.76 0.12 0.12
Matches are distributed among these distances:
240 7 0.01
241 36 0.07
242 16 0.03
243 47 0.10
244 20 0.04
245 45 0.09
246 38 0.08
247 160 0.33
248 10 0.02
249 3 0.01
250 38 0.08
251 65 0.13
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (243 bp):
AAGCCCACAACTCCGTGGCATCTTCTTCTTTAAAGCCCACAACTCCGTGGCACTCCTTTTAAAGC
CCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCAAAGCCCACAAC
TCCGTGGCACCCTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGT
GGCACCTTCTTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:573980 original size:30 final size:30
Alignment explanation
Indices: 573886--574029 Score: 134
Period size: 29 Copynumber: 4.9 Consensus size: 30
573876 TTTTCTTTTT
*** *
573886 AAGCCCACAAGTCAGTGGCATTTTTTTTCAA
1 AAGCCCACAAGTCAGTGGCA-CCCTTTTCCA
*
573917 AAGCCCACAAGTCAGTGGCAACC--TT-CA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCCA
* *
573944 AAGCCCACAAATCAGTGGCACCCTTTTCCG
1 AAGCCCACAAGTCAGTGGCACCCTTTTCCA
* *
573974 AAGCCCACAAGTCGGTGGCA-TCTTTTCCA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCCA
* * * *
574003 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGCCCACAAGTCAGTGGCACCCTTTT
574030 TCTTTTGTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
27 22 0.23
28 2 0.02
29 26 0.27
30 25 0.26
31 20 0.21
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCTTTTCCA
Found at i:574010 original size:29 final size:30
Alignment explanation
Indices: 573697--574029 Score: 146
Period size: 34 Copynumber: 10.9 Consensus size: 30
573687 GCACCCGTTT
* * *
573697 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAAGTCAGTGGCACTC-TTTT-C--CA
* *
573731 AAGCCCACAACTCCGTGGCACCTTCTTTT-CA
1 AAGCCCACAAGTCAGTGGCA-C-TCTTTTCCA
* * * *
573762 AAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT
1 AAGCCCACAAGTCAGTGGCACTC-TTTTCC---A
* * * * *
573796 AAGTCCACGACTCCGTGGCACTCTTTT-TA
1 AAGCCCACAAGTCAGTGGCACTCTTTTCCA
* * *
573825 AAGCCCACAACTCCGTGGCACCCTTTT---
1 AAGCCCACAAGTCAGTGGCACTCTTTTCCA
** * * * **
573852 AAGTGCACGACTCCGTGGCACTCTTTTTCTTTTT
1 AAGCCCACAAGTCAGTGGCACTC-TTTTC---CA
* * *
573886 AAGCCCACAAGTCAGTGGCATTTTTTTTCAA
1 AAGCCCACAAGTCAGTGGCA-CTCTTTTCCA
573917 AAGCCCACAAGTCAGTGGCAAC-C--TT-CA
1 AAGCCCACAAGTCAGTGGC-ACTCTTTTCCA
* * *
573944 AAGCCCACAAATCAGTGGCACCCTTTTCCG
1 AAGCCCACAAGTCAGTGGCACTCTTTTCCA
*
573974 AAGCCCACAAGTCGGTGGCA-TCTTTTCCA
1 AAGCCCACAAGTCAGTGGCACTCTTTTCCA
* * *
574003 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGCCCACAAGTCAGTGGCACTCTTTT
574030 TCTTTTGTAA
Statistics
Matches: 242, Mismatches: 36, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.01
27 39 0.16
28 6 0.02
29 51 0.21
30 30 0.12
31 41 0.17
32 1 0.00
33 4 0.02
34 60 0.25
35 6 0.02
36 2 0.01
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.28
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACTCTTTTCCA
Found at i:574029 original size:59 final size:57
Alignment explanation
Indices: 573917--574029 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 57
573907 TTTTTTTCAA
573917 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG
1 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG
* * * * * * *
573974 AAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTT
1 AAGCCCACAAGTCAGTGGCAAC-CTT-CAAAGCCCACAAATCAGTGGCACCCTTTT
574030 TCTTTTGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 20 0.43
58 2 0.04
59 25 0.53
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.22
Consensus pattern (57 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG
Found at i:574049 original size:35 final size:34
Alignment explanation
Indices: 574009--574075 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
573999 TCCAAAGTCC
* *
574009 ACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTT
1 ACAACTCCATAGCACTCTTTTTCTTTT-TAAGCTT
*
574044 ACAACTCTATAGCACTCTTTTTCTTTTTAAGC
1 ACAACTCCATAGCACTCTTTTTCTTTTTAAGC
574076 CCACAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.43
Consensus pattern (34 bp):
ACAACTCCATAGCACTCTTTTTCTTTTTAAGCTT
Found at i:574216 original size:49 final size:49
Alignment explanation
Indices: 574158--574667 Score: 608
Period size: 49 Copynumber: 10.7 Consensus size: 49
574148 GCAACCCTTC
* * *
574158 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574207 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C--CA---T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574250 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
574299 TAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCA-C--CA---T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574342 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
574391 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574440 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
574489 TAAGTCCATTGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574537 TAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
574580 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAGCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-CTT-CATCTT
* * *
574632 TAAGTTCAATGTAGCTCGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
574668 ACATCCTTTT
Statistics
Matches: 396, Mismatches: 44, Indels: 39
0.83 0.09 0.08
Matches are distributed among these distances:
43 112 0.28
44 2 0.01
45 1 0.00
46 5 0.01
48 45 0.11
49 195 0.49
50 1 0.00
52 35 0.09
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:574320 original size:92 final size:92
Alignment explanation
Indices: 574158--574618 Score: 673
Period size: 92 Copynumber: 5.0 Consensus size: 92
574148 GCAACCCTTC
* * *
574158 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
574223 GGCCTTGACTCAGCACATTGGCACCAT
66 GGCCTTGACTCAGCACATTGGCACCAT
*
574250 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
574315 GGCCTTGACTCAGCACATTGGCACCAT
66 GGCCTTGACTCAGCACATTGGCACCAT
574342 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
574407 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
66 GGCCTTGACTCAGCACATTGG------CACCAT
*
574440 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCATTGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
*
574505 GGCCTTGAATCAGCACATTGGCACCTCACCTT
66 GGCCTTGACTCAGCACATTGGCA-C-CA---T
* * * *
574537 TAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
* *
574596 GGCCTTGAATCAGCATATTGGCA
66 GGCCTTGACTCAGCACATTGGCA
574619 GCTTTTCCAT
Statistics
Matches: 345, Mismatches: 13, Indels: 23
0.91 0.03 0.06
Matches are distributed among these distances:
91 39 0.11
92 175 0.51
93 1 0.00
94 2 0.01
96 1 0.00
97 37 0.11
98 90 0.26
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (92 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
GGCCTTGACTCAGCACATTGGCACCAT
Found at i:574655 original size:52 final size:55
Alignment explanation
Indices: 574577--574698 Score: 160
Period size: 52 Copynumber: 2.3 Consensus size: 55
574567 ACATTGGCAC
* * * *
574577 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-GC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTCGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
574629 CTTTAAGTTCAATGTAGCTCGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTCGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
*
574684 CTTTAAGCCCAATAT
1 CTTTAAGTCCAATAT
574699 CGTTGGCCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
52 37 0.64
53 1 0.02
54 5 0.09
55 15 0.26
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTCGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:574712 original size:55 final size:52
Alignment explanation
Indices: 574577--574714 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
574567 ACATTGGCAC
* * *
574577 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAGCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
574629 CTTTAAGTTCAATGTAGCTCGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * * *
574684 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
574715 ACATATTGGC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
52 37 0.53
53 1 0.01
54 5 0.07
55 27 0.39
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:574788 original size:67 final size:68
Alignment explanation
Indices: 574680--574806 Score: 193
Period size: 67 Copynumber: 1.9 Consensus size: 68
574670 ATCCTTTTTC
* *
574680 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTTATCATCTTTTCTCA
574744 TCT
66 TCT
* * * *
574747 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTTATCATCTTT
574807 AAAACCCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
67 49 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTTATCATCTTTTCTCA
TCT
Found at i:586176 original size:12 final size:11
Alignment explanation
Indices: 586152--586226 Score: 70
Period size: 10 Copynumber: 7.0 Consensus size: 11
586142 GCGTCATCCG
586152 CAAA-AAAAAA
1 CAAACAAAAAA
586162 CAAACAAACAAA
1 CAAACAAA-AAA
586174 CAAACAAAATAA
1 CAAACAAAA-AA
*
586186 -AGA-AAAAAA
1 CAAACAAAAAA
*
586195 -AAACACAAAA
1 CAAACAAAAAA
586205 CAAAACAAAAAA
1 C-AAACAAAAAA
586217 -AAACAAAAAA
1 CAAACAAAAAA
586227 AACAACAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.07
10 23 0.42
11 6 0.11
12 22 0.40
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (11 bp):
CAAACAAAAAA
Found at i:586182 original size:22 final size:21
Alignment explanation
Indices: 586152--586231 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
586142 GCGTCATCCG
*
586152 CAAAAAAAAACAAACAAACAAA
1 CAAACAAAAACAAACAAA-AAA
* *
586174 CAAAC-AAAATAAAGAAAAAA
1 CAAACAAAAACAAACAAAAAA
*
586194 AAAACACAAAACAAAACAAAAAA
1 CAAACA-AAAAC-AAACAAAAAA
586217 -AAACAAAAA-AAACAA
1 CAAACAAAAACAAACAA
586232 CAACAAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 6 0.12
20 7 0.14
21 14 0.29
22 13 0.27
23 9 0.18
ACGTcount: A:0.82, C:0.15, G:0.01, T:0.01
Consensus pattern (21 bp):
CAAACAAAAACAAACAAAAAA
Found at i:586204 original size:10 final size:9
Alignment explanation
Indices: 586154--586231 Score: 68
Period size: 9 Copynumber: 8.2 Consensus size: 9
586144 GTCATCCGCA
586154 AAAAAAAAC
1 AAAAAAAAC
586163 AAACAAACAAAC
1 -AA-AAA-AAAC
* *
586175 AAACAAAAT
1 AAAAAAAAC
*
586184 AAAGAAAA-
1 AAAAAAAAC
*
586192 AAAAAACAC
1 AAAAAAAAC
586201 AAAACAAAAC
1 AAAA-AAAAC
586211 AAAAAAAAAC
1 -AAAAAAAAC
586221 AAAAAAAAC
1 AAAAAAAAC
586230 AA
1 AA
586232 CAACAAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.11
9 25 0.44
10 13 0.23
11 9 0.16
12 4 0.07
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:586209 original size:15 final size:14
Alignment explanation
Indices: 586154--586240 Score: 83
Period size: 15 Copynumber: 6.4 Consensus size: 14
586144 GTCATCCGCA
586154 AAAAAAAAC-AAAC
1 AAAAAAAACAAAAC
*
586167 -AAACAAAC-AAAC
1 AAAAAAAACAAAAC
* *
586179 AAAATAAAGAAAA-
1 AAAAAAAACAAAAC
*
586192 AAAAAACACAAAAC
1 AAAAAAAACAAAAC
*
586206 AAAACAAAAAAAAAC
1 AAAA-AAAACAAAAC
586221 AAAAAAAACAACAAC
1 AAAAAAAACAA-AAC
586236 AAAAA
1 AAAAA
586241 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
12 11 0.18
13 16 0.27
14 13 0.22
15 20 0.33
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:586227 original size:12 final size:12
Alignment explanation
Indices: 586153--586240 Score: 74
Period size: 12 Copynumber: 7.5 Consensus size: 12
586143 CGTCATCCGC
586153 AAAAAAAAACAA
1 AAAAAAAAACAA
* *
586165 ACAAACAAACAA
1 AAAAAAAAACAA
* *
586177 ACAAAATAAA-GA
1 A-AAAAAAAACAA
*
586189 AAAAAAAAACAC
1 AAAAAAAAACAA
*
586201 AAAACAAAAC--
1 AAAAAAAAACAA
586211 AAAAAAAAACAA
1 AAAAAAAAACAA
*
586223 AAAAAACAACAA
1 AAAAAAAAACAA
*
586235 CAAAAA
1 AAAAAA
586241 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
10 9 0.15
11 7 0.12
12 38 0.63
13 6 0.10
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:586233 original size:22 final size:21
Alignment explanation
Indices: 586153--586240 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 21
586143 CGTCATCCGC
586153 AAAAAAAAACAAACAAACAAACA
1 AAAAAAAAACAAA-AAA-AAACA
*
586176 AACAAAATAAAGAAAAAAAAAACA
1 AA-AAAA-AAA-CAAAAAAAAACA
*
586200 CAAAACAAAACAAAAAAAAACA
1 -AAAAAAAAACAAAAAAAAACA
*
586222 AAAAAAACAACAACAAAAA
1 AAAAAAA-AACAAAAAAAA
586241 GGGTCCGGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
21 6 0.11
22 21 0.38
23 5 0.09
24 12 0.22
25 8 0.15
26 3 0.05
ACGTcount: A:0.83, C:0.15, G:0.01, T:0.01
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAACA
Found at i:587710 original size:28 final size:28
Alignment explanation
Indices: 587671--587934 Score: 379
Period size: 28 Copynumber: 9.5 Consensus size: 28
587661 CTCACCTTCT
*
587671 AAAGCCCACAAGTCAGTGGCA-CATTTTT
1 AAAGCCCACAAGTCAGTGGCATC-TTTTC
587699 AAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
587727 CAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* *
587755 CAAGCCCACAAGTCAGTGGCACCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
587783 AAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
587811 AAAGCCCACAAGTCATTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
587839 AAAGCCCACAAGTCATTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* * *
587867 AAAGCCCACAAGTTAGTGGCAAC-CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* * * *
587894 AAAGCCCACAAGACAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
587922 AAAGCACACAAGT
1 AAAGCCCACAAGT
587935 TGGTGCAACC
Statistics
Matches: 218, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
27 24 0.11
28 193 0.89
29 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:587963 original size:30 final size:27
Alignment explanation
Indices: 587867--587969 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 27
587857 GCATCTTTTC
* *
587867 AAAGCCCACAAGTTAGTGGCAACCTTC-
1 AAAGCACACAAGTTGGT-GCAACCTTCA
* *** *
587894 AAAGCCCACAAGACAGTGGCAACCTTTA
1 AAAGCACACAAGTTGGT-GCAACCTTCA
587922 AAAGCACACAAGTTGGTGCAACCCTTCA
1 AAAGCACACAAGTTGGTGCAA-CCTTCA
587950 AAAGCCTACACAAGTTGGTG
1 AAAG-C-ACACAAGTTGGTG
587970 GCATCTTCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
27 28 0.44
28 22 0.34
29 1 0.02
30 13 0.20
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAGCACACAAGTTGGTGCAACCTTCA
Found at i:588038 original size:49 final size:49
Alignment explanation
Indices: 587981--588368 Score: 398
Period size: 49 Copynumber: 7.8 Consensus size: 49
587971 CATCTTCTTC
* * *
587981 TAAGTCCAATATCGCTGGCCTTGAATCAGCGCATTGGCACCCTCACCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
*
588030 TAAGTCCAATGTTGCTGGCCTTGAAACAGCACATTGGCACCCTCACCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* *
588079 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGTACCTTCACCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * *
588128 TAAGTCCAATGTTGCTGGCCTTGAATCAACACATTGGCACCTTCATCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * *
588177 TAAGTCCCATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC--C-TCACCTT
** * * * * *
588229 TAAAACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTCTTATCTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * * * * ** * *
588278 TAAGTCCGATATCGTTGCCCTCGAATCAGCATATTGGCATCTTTAACATT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA-CCCTCACCTT
* * **
588328 CCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA
1 --TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
588369 TTCTTCATCA
Statistics
Matches: 289, Mismatches: 44, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
49 211 0.73
50 7 0.02
52 71 0.25
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
Found at i:588277 original size:101 final size:98
Alignment explanation
Indices: 587976--588413 Score: 436
Period size: 98 Copynumber: 4.4 Consensus size: 98
587966 GGTGGCATCT
*
587976 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCGCATTGGCACC-CTCACCTTTAAGTCCAAT
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCACCTTTAAGTCCAAT
* *
588040 GTTGCTGGCCTTGAAACAGCACATTGGCACCCTCA
65 GTTGCTGGCCTTGAATCAGCACATTGGCA-CCTTA
* * * *
588075 CCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGTACCT-TCACCTTTAAGTCCAATG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCACCTTTAAGTCCAATG
*
588139 TTGCTGGCCTTGAATCAACACATTGGCACCTTCA
66 TTGCTGGCCTTGAATCAGCACATTGGCACCTT-A
* * * * * **
588173 TCTTTAAGTCCCATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TCACCTTTAAGTCCAA
* *
588238 TGTCGCTGGCCTTGAATCAGCATATTGGCACTCTTA
64 TGTTGCTGGCCTTGAATCAGCACATTGGCAC-CTTA
* * * * * * * * * *
588274 TCTTTAAGTCCGATATCGTTGCCCTCGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCACCTT--TAAGTCCAA
* ** *
588339 TGTCGCTGGCCTTGTCTCAGCACATTGGCATTCTTCA
64 TGTTGCTGGCCTTGAATCAGCACATTGGCA-CCTT-A
* * *
588376 TC---AAGTCTAAATGTCGCTGGCCATGAATCAGCACATTG
1 TCTTTAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTG
588414 TCATTCTTCG
Statistics
Matches: 283, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
97 3 0.01
98 121 0.43
99 13 0.05
100 23 0.08
101 117 0.41
102 6 0.02
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (98 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCACCTTTAAGTCCAATG
TTGCTGGCCTTGAATCAGCACATTGGCACCTTA
Found at i:589182 original size:19 final size:19
Alignment explanation
Indices: 589136--589252 Score: 78
Period size: 19 Copynumber: 6.7 Consensus size: 19
589126 TTTCAACAAT
*
589136 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-A
*
589157 ATGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
*
589176 TTGTATCCATAC---A--A
1 TTGTATCGATACATAAGTA
589190 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
*
589208 TTGTATCCATAC---A--A
1 TTGTATCGATACATAAGTA
*
589222 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
*
589240 TTGTATCTATACA
1 TTGTATCGATACA
589253 ATGTATCGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
13 20 0.27
14 2 0.03
16 4 0.05
18 1 0.01
19 32 0.43
20 3 0.04
21 13 0.17
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:589197 original size:32 final size:32
Alignment explanation
Indices: 589156--589260 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
589146 ACAAACAGTA
589156 AATGTATCGATACATAAGTATTGTATCCATAC
1 AATGTATCGATACATAAGTATTGTATCCATAC
589188 AATGTATCGATACATAAGTATTGTATCCATAC
1 AATGTATCGATACATAAGTATTGTATCCATAC
* *
589220 AATGTATCGATACATAAGTGTTGTATCTATAC
1 AATGTATCGATACATAAGTATTGTATCCATAC
589252 AATGTATCG
1 AATGTATCG
589261 CTATAATGCT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTATTGTATCCATAC
Found at i:589322 original size:13 final size:13
Alignment explanation
Indices: 589304--589331 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
589294 CATTATTCAA
589304 TGTATCGATACAT
1 TGTATCGATACAT
589317 TGTATCGATACAT
1 TGTATCGATACAT
589330 TG
1 TG
589332 ATCATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:589326 original size:33 final size:33
Alignment explanation
Indices: 589284--589349 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
589274 GCCAAGGATA
*
589284 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATATATCGATACAT
*
589317 TGTATCGATACATTGATCATTATATCGATACAT
1 TGTATCGATACATTGATCAATATATCGATACAT
589350 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATATATCGATACAT
Found at i:591817 original size:20 final size:21
Alignment explanation
Indices: 591794--591845 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
591784 AGATTGCACA
*
591794 GTATCGATACATG-ACCA-AAT
1 GTATCGATACATGCA-AAGAAT
* *
591814 GTATCAATACTTGCAAAGAAT
1 GTATCGATACATGCAAAGAAT
591835 GTATCGATACA
1 GTATCGATACA
591846 GGTCATTGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (21 bp):
GTATCGATACATGCAAAGAAT
Found at i:594377 original size:119 final size:117
Alignment explanation
Indices: 594169--594384 Score: 253
Period size: 119 Copynumber: 1.8 Consensus size: 117
594159 GGGTGTCCAC
* * * *
594169 TTTTCAAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAAGACCAAGGAAGAGAAGA
1 TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
594234 AAAGGAAAGTGTCCTGCTTCTTGAGGA-TAAAGTGAAAAAGAGTACGTCCCA
66 AAAGGAAAGTGTCCTGCTTCTTGAGGACTAAAGTGAAAAAGAGTACGTCCCA
* *
594285 TTTTCCAAGGACAAAGGAAAAAGGGAAATGAAATACGTCCTGCT-CTCTGAGGACAAAAGAA-AG
1 TTTT-CAAGGACAAAGG-AAAAGAG-AATGAAATACGTCCTGCTCCT-TGAAGACAAAAGAAGAG
* * *
594348 AGGATAA-TAAAGTGTATCCTGC-TCTTTGAGGACTAAA
62 AAGAAAAGGAAAGTG--TCCTGCTTC-TTGAGGACTAAA
594385 AAGTGCCACC
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
116 4 0.05
117 18 0.22
118 17 0.20
119 40 0.48
120 4 0.05
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (117 bp):
TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
AAAGGAAAGTGTCCTGCTTCTTGAGGACTAAAGTGAAAAAGAGTACGTCCCA
Found at i:594551 original size:26 final size:26
Alignment explanation
Indices: 594522--594609 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
594512 GTGGGCTTTA
594522 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
594548 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
*
594577 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
594603 AAAGGTG
1 AAAGGTG
594610 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.13
28 6 0.13
29 11 0.23
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:594918 original size:61 final size:60
Alignment explanation
Indices: 594364--595197 Score: 998
Period size: 55 Copynumber: 14.3 Consensus size: 60
594354 ATAAAGTGTA
* * *
594364 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
594419 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
594474 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACATGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
594529 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
594584 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
594645 TGCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
594704 TCCCGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
594763 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGACG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
594822 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
594882 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTCGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
594943 TCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
*
595004 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG-G
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * *
595059 TCCTGCTCTTTGGGGACGGAACGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
595119 TCCCACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
595180 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
595198 AAAAAGCGGA
Statistics
Matches: 704, Mismatches: 48, Indels: 48
0.88 0.06 0.06
Matches are distributed among these distances:
54 6 0.01
55 230 0.33
56 6 0.01
57 1 0.00
59 171 0.24
60 92 0.13
61 196 0.28
62 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:596205 original size:12 final size:12
Alignment explanation
Indices: 596188--596219 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
596178 TCTCCTTTTC
596188 TTTGTTTTGTTT
1 TTTGTTTTGTTT
596200 TTTGTTTTGTTT
1 TTTGTTTTGTTT
596212 TTT-TTTTG
1 TTTGTTTTG
596220 AAGAGAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:596210 original size:17 final size:16
Alignment explanation
Indices: 596188--596219 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
596178 TCTCCTTTTC
596188 TTTGTTTTGTTTTTTGT
1 TTTGTTTT-TTTTTTGT
596205 TTTGTTTTTTTTTTG
1 TTTGTTTTTTTTTTG
596220 AAGAGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (16 bp):
TTTGTTTTTTTTTTGT
Found at i:608782 original size:28 final size:28
Alignment explanation
Indices: 608742--608813 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
608732 GGAATAAAGC
*
608742 CGGGGTTGGAGTATCCCCTCA-GAAGTAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
*
608770 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
* *
608798 CGAGGTTGAAGTATCC
1 CGGGGTTGGAGTATCC
608814 TCAATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:608865 original size:52 final size:51
Alignment explanation
Indices: 608802--609190 Score: 202
Period size: 51 Copynumber: 7.4 Consensus size: 51
608792 AAATAACGAG
* * * *
608802 GTTGAAGTATCCTCAATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAATCGGA
* * * *
608854 GTTGGAGTATCCTCGATTAAAG-GAAAAATTGGTGTTTCGAAAATAAAA-CCGA
1 GTTGGAGTATCCTCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * * *
608906 GGTTGGAGTATCCTCGATTGTGGAATAATTAGTGTTTTAGCAATAAAACCGGG
1 -GTTGGAGTATCCTCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * * ** * * *
608959 GTTGGAGTATCCCCGATTATGAAAAATCAATACTTTGGAAATACAGTCGGG
1 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * * ** * * *
609010 GTTGGAGTATCC-C-CTCG-GAAATAACGGGGTTGGAGTTTCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCTCGATTGTGAAA-AA-----TTAGTGTTT--TGGA-AATAAAATCGGA
* *
609065 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAATCGGA
* *
609119 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTT-GAAGATAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGA-AAAATTAGTGTTTTGGAA-ATAAAATCGGA
* *
609170 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCTCGATTGTG
609191 GAGAATTGAG
Statistics
Matches: 258, Mismatches: 52, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 5 0.02
51 66 0.26
52 59 0.23
53 50 0.19
54 37 0.14
55 20 0.08
56 4 0.02
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
Found at i:609040 original size:28 final size:27
Alignment explanation
Indices: 609006--609080 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
608996 GAAATACAGT
**
609006 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGG-AATAA
* * *
609034 CGGGGTTGGAGTTTCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGAGGAATAA
609061 CGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
609081 TTGTGAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGGAATAA
Found at i:609171 original size:51 final size:53
Alignment explanation
Indices: 608802--609187 Score: 174
Period size: 52 Copynumber: 7.3 Consensus size: 53
608792 AAATAACGAG
* * * * * *
608802 GTTGAAGTATCCTCAATTGTGAA-AAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGGAAATAAAATCGGA
* * * * * *
608854 GTTGGAGTATCCTCGATTAAAGGAA-AAATTGGTG-TTTCGAAAATAAAA-CCGA
1 GTTGGAGTATCCCCGATT--ATGAAGAAATTAGTGTTTTTGGAAATAAAATCGGA
* * * * * * *
608906 GGTTGGAGTATCCTCGATTGTGGAA-TAATTAGTG-TTTTAGCAATAAAACCGGG
1 -GTTGGAGTATCCCCGATTAT-GAAGAAATTAGTGTTTTTGGAAATAAAATCGGA
* * ** * * *
608959 GTTGGAGTATCCCCGATTATGAA-AAATCAAT-ACTTTGGAAATACAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGGAAATAAAATCGGA
* *** * * *** * * *
609010 GTTGGAGTATCCCCTCGGA-AAT-AACGGGGTTGGAGTTTCCCCGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-C-GATTATGAA-GAAATTAGTGTTT-TTGGA-AATAAAATCGGA
* *
609065 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGGAAATAAAATCGGA
609119 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTT-GAAGATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGGAA-ATAAAATCGGA
*
609170 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
609188 GTGGAGAATT
Statistics
Matches: 253, Mismatches: 60, Indels: 43
0.71 0.17 0.12
Matches are distributed among these distances:
50 3 0.01
51 63 0.25
52 68 0.27
53 55 0.22
54 44 0.17
55 15 0.06
56 3 0.01
57 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGGAAATAAAATCGGA
Found at i:611003 original size:10 final size:10
Alignment explanation
Indices: 610990--611019 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
610980 CAATGGAATA
610990 GTGTTTTTTT
1 GTGTTTTTTT
611000 GTGTTTTTTT
1 GTGTTTTTTT
611010 G-GTTTTTTT
1 GTGTTTTTTT
611019 G
1 G
611020 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:611571 original size:13 final size:13
Alignment explanation
Indices: 611553--611578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
611543 ACAAAGATCC
611553 ATGTATCGATACA
1 ATGTATCGATACA
611566 ATGTATCGATACA
1 ATGTATCGATACA
611579 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:611574 original size:33 final size:33
Alignment explanation
Indices: 611532--611598 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
611522 AAAATTTCCA
***
611532 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
611565 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
611598 A
1 A
611599 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:611642 original size:19 final size:19
Alignment explanation
Indices: 611618--611672 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
611608 CAGTAGCTAA
*
611618 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
611637 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
611656 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
611673 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:612356 original size:84 final size:84
Alignment explanation
Indices: 612201--612365 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
612191 CATTTTCCAC
* * * *
612201 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
612266 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
612285 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
612347 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
612366 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:613928 original size:34 final size:35
Alignment explanation
Indices: 613890--613956 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
613880 CCTTACAACA
613890 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
613924 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
613957 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:614447 original size:19 final size:20
Alignment explanation
Indices: 614407--614447 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
614397 TGAACAGTGA
**
614407 TGTATCGATACTATTTATAG
1 TGTATCGATACTATGAATAG
614427 TGTATCGATAC-ATGAATAG
1 TGTATCGATACTATGAATAG
614446 TG
1 TG
614448 ATGAACAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACTATGAATAG
Found at i:617235 original size:160 final size:159
Alignment explanation
Indices: 616993--617486 Score: 502
Period size: 158 Copynumber: 3.1 Consensus size: 159
616983 AGATTAGAGA
* * * * * **
616993 ATCCCCGA-TGATG-AAAAGTTGATATTTTGCAAACAAAATCAGGGTTGGAGTAT-CCTATCGAA
1 ATCCCCGATTG-TGAAAAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCT-TAAAA
* * * * *
617055 AATAA-CAGGGTTGGAGTATCCCTGATGGTGAAAAATCAGTGTCTTAGAAATAAAATCGGGGTTA
64 AATAATGA-GGTTAGAGTATCCCTGATTGTGAAAAATCAGTGTCTTAGAAATAAAACCAGGGTTA
617119 GAGTATCCCCTCGAAAATAACGGGGTTGGAGT
128 GAGTATCCCCTCGAAAATAACGGGGTTGGAGT
*
617151 ATCCCCGATTGTGAAAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCTTAAAAA
1 ATCCCCGATTGTG-AAAAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCTTAAAAA
* * *
617216 ATAATGACGTTAGAGTATCCCGGATTGTGAAAAATC-GATG-CTTCAAAAATAAAACCAGGGTTA
65 ATAATGAGGTTAGAGTATCCCTGATTGTGAAAAATCAG-TGTCTT-AGAAATAAAACCAGGGTTA
** *
617279 GAGTATTTCCT-TAGAAATAACGGGGTTGGAGT
128 GAGTATCCCCTCGA-AAATAACGGGGTTGGAGT
* * * * * *
617311 TTCCCCGATTATG-AAAACTTGGTGTTTTGAAAATAAAATCGGGGTTGGAGCATCCCCTAAAAAA
1 ATCCCCGATTGTGAAAAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCTTAAAAAA
* * * * * * *
617375 TAATGGGGTTAGAGTATCTCTGATTGTGGAAAATTAGTGT-TTTGAAAATAAAACCAAGGTTGGA
66 TAATGAGGTTAGAGTATCCCTGATTGTGAAAAATCAGTGTCTTAG-AAATAAAACCAGGGTTAGA
* * * *
617439 GAATCCTCTCGGAAATAACGGGGTTAGAGT
130 GTATCCCCTCGAAAATAACGGGGTTGGAGT
* * *
617469 ATCCTCGATGGTGGAAAA
1 ATCCCCGATTGTGAAAAA
617487 TCGATATTTT
Statistics
Matches: 277, Mismatches: 46, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
158 137 0.49
159 12 0.04
160 124 0.45
161 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (159 bp):
ATCCCCGATTGTGAAAAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCTTAAAAAA
TAATGAGGTTAGAGTATCCCTGATTGTGAAAAATCAGTGTCTTAGAAATAAAACCAGGGTTAGAG
TATCCCCTCGAAAATAACGGGGTTGGAGT
Found at i:617483 original size:79 final size:79
Alignment explanation
Indices: 617017--617487 Score: 355
Period size: 79 Copynumber: 5.9 Consensus size: 79
617007 AAAGTTGATA
* * * * * * *
617017 TTTTGCAAACAAAATCAGGGTTGGAGTATCCTATCGAAAATAACAGGGTTGGAGTATCCCTGATG
1 TTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAACGGGGTTAGAGTATCCCTGATT
* *
617082 GTGAAAAATCAGTG
66 GTGGAAAATTAGTG
* * * * * * *
617096 TCTT-AGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1 TTTTGA-AAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAACGGGGTTAGAGTATCCCTGAT
*
617160 TGTGAAAAAAATT-GATG
65 TGTG--GAAAATTAG-TG
* * * * ** *
617177 TTTTGGAAATAAAATCGGGGTTGGAGTATCC-CTTAAAAAATAATGACGTTAGAGTATCCCGGAT
1 TTTTGAAAATAAAATCAGGGTTGGAGTATCCTC-TCAAAAATAACGGGGTTAGAGTATCCCTGAT
* *
617241 TGT-GAAAAATCGATG
65 TGTGGAAAATTAG-TG
* ** * * * * * *
617256 CTTCAAAAATAAAACCAGGGTTAGAGTATTTCCT-T-AGAAATAACGGGGTTGGAGTTTCCCCGA
1 TTTTGAAAATAAAATCAGGGTTGGAGTA--TCCTCTCAAAAATAACGGGGTTAGAGTATCCCTGA
* *
617319 TTAT-GAAAACTTGGTG
64 TTGTGGAAAA-TTAGTG
* * * * * *
617335 TTTTGAAAATAAAATCGGGGTTGGAGCATCCCCTAAAAAATAATGGGGTTAGAGTATCTCTGATT
1 TTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAACGGGGTTAGAGTATCCCTGATT
617400 GTGGAAAATTAGTG
66 GTGGAAAATTAGTG
* * * **
617414 TTTTGAAAATAAAACCAAGGTTGGAGAATCCTCTCGGAAATAACGGGGTTAGAGTAT-CCTCGAT
1 TTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAACGGGGTTAGAGTATCCCT-GAT
*
617478 GGTGGAAAAT
65 TGTGGAAAAT
617488 CGATATTTTA
Statistics
Matches: 310, Mismatches: 67, Indels: 30
0.76 0.16 0.07
Matches are distributed among these distances:
77 3 0.01
78 8 0.03
79 224 0.72
80 10 0.03
81 65 0.21
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
TTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAACGGGGTTAGAGTATCCCTGATT
GTGGAAAATTAGTG
Found at i:619927 original size:20 final size:20
Alignment explanation
Indices: 619890--619927 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
619880 TACATTTGAG
*
619890 TAAAACTCAAAATGTATCAA
1 TAAAACTCAAAATATATCAA
619910 TAAAA-TCAAGAATATATC
1 TAAAACTCAA-AATATATC
619928 GATACAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAAACTCAAAATATATCAA
Found at i:620613 original size:40 final size:39
Alignment explanation
Indices: 620527--620780 Score: 198
Period size: 41 Copynumber: 6.3 Consensus size: 39
620517 AAGGGCATCC
* *
620527 TGCTCTTTGAGGATAAAGGAAAAG-GAGT--A--CGTCT
1 TGCTCTTTGAGGACAAAGGAAAAGAGAATAAATGCGTCT
* *
620561 TGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGGTCT
1 TGCTCTTTGAGGACAAAGGAAAAGAGAAT-AAATGCGTCT
* * *
620601 TGCTCCTTGAGGACAAA-GAAAAAAGTAGATAAAATGCATCT
1 TGCTCTTTGAGGACAAAGGAAAAGAG-A-AT-AAATGCGTCT
* * * *
620642 TACTCTTTGAGGACAAAGGAAAAGAAAGAAGTTAAGTGTGTCC
1 TGCTCTTTGAGGACAAAGGAAAAG--AGAA--TAAATGCGTCT
*
620685 TGCTCTTTGAGGACAAAGGAGAAA-AGGAAATAAAGTGCATCT
1 TGCTCTTTGAGGACAAAGGA-AAAGA-G-AATAAA-TGCGTCT
* * *
620727 TGCTTTTTGAGGACAAAGGGAAAAGAAAATACAGTGCGTCT
1 TGCTCTTTGAGGACAAA-GGAAAAGAGAATA-AATGCGTCT
620768 TGCTCTTTGAGGA
1 TGCTCTTTGAGGA
620781 TAAAAGAGAA
Statistics
Matches: 173, Mismatches: 27, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
34 22 0.13
35 3 0.02
38 1 0.01
39 7 0.04
40 20 0.12
41 51 0.29
42 31 0.18
43 32 0.18
44 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (39 bp):
TGCTCTTTGAGGACAAAGGAAAAGAGAATAAATGCGTCT
Found at i:620652 original size:41 final size:41
Alignment explanation
Indices: 620556--620796 Score: 213
Period size: 41 Copynumber: 5.8 Consensus size: 41
620546 AAAAGGAGTA
*
620556 CGTCTTGCTCTTCGAGGACAAAG-GAAAAG-AGAATGAAA-TG
1 CGTCTTGCTCTTTGAGGACAAAGAGAAAAGAAG-AT-AAAGTG
* * * * *
620596 GGTCTTGCTCCTTGAGGACAAAGAAAAAAGTAGATAAAATG
1 CGTCTTGCTCTTTGAGGACAAAGAGAAAAGAAGATAAAGTG
* * *
620637 CATCTTACTCTTTGAGGACAAAG-GAAAAGAAAGAAGTTAAGTG
1 CGTCTTGCTCTTTGAGGACAAAGAGAAAAG-AAG-A-TAAAGTG
* *
620680 TGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAA-ATAAAGTG
1 CGTCTTGCTCTTTGAGGACAAA-GAGAAAA-GAAGATAAAGTG
* * * * *
620722 CATCTTGCTTTTTGAGGACAAAGGGAAAAGAAAATACAGTG
1 CGTCTTGCTCTTTGAGGACAAAGAGAAAAGAAGATAAAGTG
* *
620763 CGTCTTGCTCTTTGAGGATAAAAGAGAAAGGAAG
1 CGTCTTGCTCTTTGAGGA-CAAAGAGAAAAGAAG
620797 GAAATGAAGT
Statistics
Matches: 161, Mismatches: 29, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
40 31 0.19
41 59 0.37
42 38 0.24
43 24 0.15
44 1 0.01
45 7 0.04
46 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.22
Consensus pattern (41 bp):
CGTCTTGCTCTTTGAGGACAAAGAGAAAAGAAGATAAAGTG
Found at i:620698 original size:43 final size:43
Alignment explanation
Indices: 620561--620826 Score: 185
Period size: 41 Copynumber: 6.3 Consensus size: 43
620551 GAGTACGTCT
* ** *
620561 TGCTCTTCGAGGACAAAGGAAAAG--AG-AATGAAA-TGGGTCT
1 TGCTCTTTGAGGACAAAGGAAAAGAAAGAAAT-AAAGTGCATCC
* * * *
620601 TGCTCCTTGAGGACAAA-G-AAA-AAAGTAGATAAAATGCATCT
1 TGCTCTTTGAGGACAAAGGAAAAGAAAG-AAATAAAGTGCATCC
* * * **
620642 TACTCTTTGAGGACAAAGGAAAAGAAAGAAGTTAAGTGTGTCC
1 TGCTCTTTGAGGACAAAGGAAAAGAAAGAAATAAAGTGCATCC
* * *
620685 TGCTCTTTGAGGACAAAGGAGAA-AAGGAAATAAAGTGCATCT
1 TGCTCTTTGAGGACAAAGGAAAAGAAAGAAATAAAGTGCATCC
* * * *
620727 TGCTTTTTGAGGACAAAGGGAAAAG--A-AAATACAGTGCGTCT
1 TGCTCTTTGAGGACAAA-GGAAAAGAAAGAAATAAAGTGCATCC
* * * *
620768 TGCTCTTTGAGGATAAAAGAGAAAGGAAGGAAATGAAGTGCATCC
1 TGCTCTTTGAGGA-CAAAG-GAAAAGAAAGAAATAAAGTGCATCC
*
620813 TGCTCTTTAAGGAC
1 TGCTCTTTGAGGAC
620827 TAAAAGGTTC
Statistics
Matches: 174, Mismatches: 37, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
38 3 0.02
39 3 0.02
40 18 0.10
41 48 0.28
42 38 0.22
43 37 0.21
44 4 0.02
45 23 0.13
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (43 bp):
TGCTCTTTGAGGACAAAGGAAAAGAAAGAAATAAAGTGCATCC
Found at i:620807 original size:86 final size:81
Alignment explanation
Indices: 620558--620826 Score: 272
Period size: 85 Copynumber: 3.2 Consensus size: 81
620548 AAGGAGTACG
* * * * * *
620558 TCTTGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGGTCTTGCTCCTTGAGGACAAAGA-AA
1 TCTTGCTCTTTGAGGACAAAGGAAAAGAAAAT-AAGTGCGTCTTGCTCTTTGAGGAAAAAGAGAA
* * *
620622 AAAGTAGATAAAATGCA
65 AAAGGAAATAAAGTGCA
* * * *
620639 TCTTACTCTTTGAGGACAAAGGAAAAGAAAGAAGTTAAGTGTGTCCTGCTCTTTGAGGACAAAG-
1 TCTTGCTCTTTGAGGACAAAGGAAAAG-AA-AA--TAAGTGCGTCTTGCTCTTTGAGGAAAAAGA
620703 GAGAAAAGGAAATAAAGTGCA
62 GA-AAAAGGAAATAAAGTGCA
*
620724 TCTTGCTTTTTGAGGACAAAGGGAAAAGAAAATACAGTGCGTCTTGCTCTTTGAGGATAAAAGAG
1 TCTTGCTCTTTGAGGACAAA-GGAAAAGAAAATA-AGTGCGTCTTGCTCTTTGAGGA-AAAAGAG
*
620789 AAAGGAAGGAAATGAAGTGCA
63 AAA--AAGGAAATAAAGTGCA
* *
620810 TCCTGCTCTTTAAGGAC
1 TCTTGCTCTTTGAGGAC
620827 TAAAAGGTTC
Statistics
Matches: 157, Mismatches: 19, Indels: 19
0.81 0.10 0.10
Matches are distributed among these distances:
81 25 0.16
82 3 0.02
83 22 0.14
84 33 0.21
85 38 0.24
86 36 0.23
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (81 bp):
TCTTGCTCTTTGAGGACAAAGGAAAAGAAAATAAGTGCGTCTTGCTCTTTGAGGAAAAAGAGAAA
AAGGAAATAAAGTGCA
Found at i:620966 original size:61 final size:59
Alignment explanation
Indices: 620810--621260 Score: 422
Period size: 61 Copynumber: 7.4 Consensus size: 59
620800 ATGAAGTGCA
* * * *
620810 TCCTGCTCTTTAAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTT-AGAAGGAAAAAAGAAAG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGA-AAGG--AAAAG--CG
* * * * *
620874 TATCCTACTCTTTGGGGACTAAAAGGTGCCACCAATTTGTGTGGGCTTTGCAAGGAGAAAGCG
1 --TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAAGCG
* *
620937 TCCTGCTCTTTGAAGATTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-CG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCG
* * * ** * * *
620996 TCCTGCTCTTTGAAGACTAAAAGGTACTGCCAACTTGTGTGGGCTTTAAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-GCG
* * * * *
621057 CCCTGCTTTTTGAGGATTGAAAGGTGCCACTAATTTGTGTGGGCTTTGAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-GCG
* * * *
621118 CCCTACTCTTTGAGGACTGGAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGCCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG-CG
* * * *
621179 TCTTGCTCTTTGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTGAAAGG-AAAGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCG
*
621238 TGCTGCTCTTTGAGGACTGAAAG
1 TCCTGCTCTTTGAGGACTGAAAG
621261 GATAAAAGGT
Statistics
Matches: 324, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
58 7 0.02
59 65 0.20
60 8 0.02
61 185 0.57
62 7 0.02
63 1 0.00
64 1 0.00
65 4 0.01
66 46 0.14
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCG
Found at i:621141 original size:181 final size:181
Alignment explanation
Indices: 620810--621261 Score: 552
Period size: 181 Copynumber: 2.5 Consensus size: 181
620800 ATGAAGTGCA
* * * *
620810 TCCTGCTCTTT-AAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTTAGAAGGAAAAAAGAAAG
1 TCCTGCTCTTTGAA-GACTAAAAGGTACTACCAACTTGTGTGGGCTTT--AA--AAAGAA-AATG
* * * * * *
620874 TATCCTACTCTTTGGGGACTAAAAGGTGCCACCAATTTGTGTGGGCTTTGCAAGGAGAAAGCGTC
60 T-GCCTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGAGAAAGCGCC
* * *
620939 CTGCTCTTTGAAGATTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-CG
124 CTACTCTTTGAAGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAACCG
*
620996 TCCTGCTCTTTGAAGACTAAAAGGTACTGCCAACTTGTGTGGGCTTTAAAAAGAAAATGTGCCCT
1 TCCTGCTCTTTGAAGACTAAAAGGTACTACCAACTTGTGTGGGCTTTAAAAAGAAAATGTG-CCT
* * *
621061 GCTTTTTGAGGATTGAAAGGTGCCACTAATTTGTGTGGGCTTTGAAAGGA-AAAGGCGCCCTACT
65 GCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGAGAAA-GCGCCCTACT
* *
621125 CTTTGAGGACTGGAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGCCG
129 CTTTGAAGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-CCG
* * * * * * *
621179 TCTTGCTCTTTGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTGAAAGGAAAGTGTG-CTG
1 TCCTGCTCTTTGAAGACTAAAAGGTACTACCAACTTGTGTGGGCTTTAAAAAGAAAATGTGCCTG
621243 CTCTTTGAGGACTGAAAGG
66 CTCTTTGAGGACTGAAAGG
621262 ATAAAAGGTT
Statistics
Matches: 232, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
180 3 0.01
181 124 0.53
182 5 0.02
183 55 0.24
184 2 0.01
186 41 0.18
187 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (181 bp):
TCCTGCTCTTTGAAGACTAAAAGGTACTACCAACTTGTGTGGGCTTTAAAAAGAAAATGTGCCTG
CTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGAGAAAGCGCCCTACTCT
TTGAAGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAACCG
Found at i:623294 original size:13 final size:13
Alignment explanation
Indices: 623275--623305 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
623265 ACAATTCATC
623275 ATGTATCGATACA
1 ATGTATCGATACA
*
623288 TTGTATCGATACA
1 ATGTATCGATACA
623301 ATGTA
1 ATGTA
623306 CCATGTGTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:623375 original size:20 final size:19
Alignment explanation
Indices: 623350--623422 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
623340 CTGCCAGTTT
**
623350 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
623370 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
623389 CATGTATAGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
623410 -ATGTATCGATACA
1 CATGTATCGATACA
623423 TCTAGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:623940 original size:14 final size:14
Alignment explanation
Indices: 623921--623947 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
623911 ATCAGAAAAG
623921 TTTAGATATCAAAT
1 TTTAGATATCAAAT
623935 TTTAGATATCAAA
1 TTTAGATATCAAA
623948 GTTTCATTTT
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTAGATATCAAAT
Found at i:624025 original size:30 final size:31
Alignment explanation
Indices: 623989--624046 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
623979 TAAGGCTCTC
*
623989 GTTAAAAA-AATTTCTCCCCTTTGATAATCG
1 GTTAAAAAGAATTTCTCCCCCTTGATAATCG
*
624019 GTTAAAAAGACTTTCTCCCCCTTGATAA
1 GTTAAAAAGAATTTCTCCCCCTTGATAA
624047 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (31 bp):
GTTAAAAAGAATTTCTCCCCCTTGATAATCG
Found at i:630321 original size:48 final size:47
Alignment explanation
Indices: 630212--630750 Score: 431
Period size: 48 Copynumber: 11.9 Consensus size: 47
630202 ATATTAAAGA
* * * * *
630212 TGCCAATATGCTGATTGAAGGCCAACGATATCGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG--CAAGG
* * *
630261 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG-CAAGG
* * *
630309 TCCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT------A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGCAAGG
* * * *
630348 TGCCAATGTGCTAATTCAAGGCCAGCGACATTTGTCTTAAAGCTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGC--AAGG
*
630397 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--------G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGCAAGG
* * *
630436 TGCCAATGTGTTGATTCAAGGCCAGCGATATTGGTCTTAAAGGCAAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAA-GCAAGG
** *
630484 TGCCAATATGCTGATTCAAGGCCAATGATATTGGGC-T-----AA--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGCAAGG
* * *
630523 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG-CAAGG
*
630571 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT------A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGCAAGG
* *
630610 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG-CAAGG
* * * *
630658 TGCCAAAATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA-A--G-CAAGG
* * *
630709 TGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG
630751 GCGCCACAGA
Statistics
Matches: 393, Mismatches: 57, Indels: 81
0.74 0.11 0.15
Matches are distributed among these distances:
39 133 0.34
40 1 0.00
41 4 0.01
46 3 0.01
47 2 0.01
48 139 0.35
49 69 0.18
50 1 0.00
51 41 0.10
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (47 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGCAAGG
Found at i:630365 original size:39 final size:39
Alignment explanation
Indices: 630311--630648 Score: 244
Period size: 39 Copynumber: 7.9 Consensus size: 39
630301 AGACAAGGTC
*
630311 CCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
* * * * *
630350 CCAATGTGCTAATTCAAGGCCAGCGACATTTGTCTTAAAGCTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATA-TTG------GGCT-TA--TG
*
630399 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
* * *
630438 CCAATGTGTTGATTCAAGGCCAGCGATATTGGTCTTAAAGGCAAGTTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-------A--TG
** *
630486 CCAATATGCTGATTCAAGGCCAATGATATTGGGCTAATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
* * *
630525 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAATGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-------A--TG
*
630573 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
* * *
630612 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
630649 AAGACAAGGT
Statistics
Matches: 237, Mismatches: 34, Indels: 56
0.72 0.10 0.17
Matches are distributed among these distances:
39 127 0.54
40 3 0.01
41 2 0.01
42 3 0.01
46 4 0.02
47 1 0.00
48 70 0.30
49 27 0.11
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (39 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
Found at i:630694 original size:87 final size:87
Alignment explanation
Indices: 630261--630691 Score: 693
Period size: 87 Copynumber: 4.9 Consensus size: 87
630251 AAGATGAAGG
* *
630261 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGAAGACAAGGTCCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
630326 AAGGCCAGCAATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
630348 TGCCAATGTGCTAATTCAAGGCCAGCGACATTTGTCTTAAAG-CTGAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC--AAGGTGCCAATATGCTGAT
*
630412 TCAAGGCCAGCGATATTGGGCTTG
64 TCAAGGCCAGCGATATTGGGCTTA
* * * *
630436 TGCCAATGTGTTGATTCAAGGCCAGCGATATTGGTCTTAAAGGCAAGTTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
** *
630501 AAGGCCAATGATATTGGGCTAA
66 AAGGCCAGCGATATTGGGCTTA
*
630523 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAATGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
630588 AAGGCCAGCGATATTGGACTTA
66 AAGGCCAGCGATATTGGGCTTA
*
630610 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAAAATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
630675 AAGGCCAGCGATATTGG
66 AAGGCCAGCGATATTGG
630692 ACTCAAGATG
Statistics
Matches: 315, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
86 1 0.00
87 235 0.75
88 78 0.25
89 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:630730 original size:51 final size:48
Alignment explanation
Indices: 630610--630750 Score: 167
Period size: 51 Copynumber: 2.9 Consensus size: 48
630600 ATTGGACTTA
* * * *
630610 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAAGACAAGG
*
630658 TGCCAAAATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGTA-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAA-A--G-ACAAGG
* * *
630709 TGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAAG
630751 GCGCCACAGA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
48 36 0.45
49 1 0.01
50 1 0.01
51 41 0.51
52 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (48 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAAGACAAGG
Found at i:630805 original size:34 final size:34
Alignment explanation
Indices: 630753--631032 Score: 252
Period size: 34 Copynumber: 8.7 Consensus size: 34
630743 ACTTAAAGGC
* *
630753 GCCACAGAGTTGTAGACTTAAAAGGAAAAAGAGT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
* *
630787 GCCACGGAGTCGTGGACTTAAAAGGAAAATGA-T
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
*
630820 GCCACGGGGTTGTGGACTT------AAAAAG-GT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
* * * *
630847 GCCACGTAGTCGAGGACTTAAAAGGAACAAGAGT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
* * * *
630881 GCCACAGAGTCGTGGACTTAAAA--AGAAAGGGT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
* * *
630913 GCCACGGAGATGTGGACTTAAAAGGAACAAGGGT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
* * *
630947 GCTATGGAGTTGTGGGCTTAAAA-G-----G-GT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
*
630974 GCCACGGAGTTGTGGACTTTAAAGGAAAAAGAGT
1 GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
*
631008 GCCACGGAGTTGTGGGCTTAAAAGG
1 GCCACGGAGTTGTGGACTTAAAAGG
631033 GTGCCACGAA
Statistics
Matches: 196, Mismatches: 33, Indels: 34
0.75 0.13 0.13
Matches are distributed among these distances:
27 42 0.21
28 2 0.01
32 26 0.13
33 25 0.13
34 101 0.52
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (34 bp):
GCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
Found at i:630971 original size:27 final size:27
Alignment explanation
Indices: 630941--631107 Score: 147
Period size: 27 Copynumber: 5.9 Consensus size: 27
630931 TAAAAGGAAC
* * *
630941 AAGGGTGCTATGGAGTTGTGGGCTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
630968 AAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAA
1 AAGGGTGCCACGGAGTTGTGGAC-TT------AA
* *
631002 AAGAGTGCCACGGAGTTGTGGGCTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
631029 AAGGGTGCCACGAAGTTATGGACAT-A
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
631055 CAGGGTTGTCACGGAGCTGTGGACTTAA
1 AAGGG-TGCCACGGAGTTGTGGACTTAA
*
631083 AAGGGTGCCACAGAGTTGTGGACTT
1 AAGGGTGCCACGGAGTTGTGGACTT
631108 TGAAAAGAGA
Statistics
Matches: 111, Mismatches: 20, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
26 5 0.05
27 74 0.67
28 7 0.06
33 2 0.02
34 23 0.21
ACGTcount: A:0.27, C:0.14, G:0.36, T:0.23
Consensus pattern (27 bp):
AAGGGTGCCACGGAGTTGTGGACTTAA
Found at i:630998 original size:127 final size:127
Alignment explanation
Indices: 630753--631031 Score: 355
Period size: 127 Copynumber: 2.2 Consensus size: 127
630743 ACTTAAAGGC
* *
630753 GCCACAGAGTTGTAGACTTAAAAGGAAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAATG
1 GCCACAGAGTTGTGGACTTAAAA-GAAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAGG
* * *
630818 ATGCCACGGGGTTGTGGACTTAAAAAGGTGCCACGTAGTCGAGGACTTAAAAGGAACAAGAGT
65 ATGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTCGAGGACTTAAAAGGAAAAAGAGT
* * *
630881 GCCACAGAGTCGTGGACTTAAAA-AGAAAGGGTGCCACGGAGAT-GTGGACTTAAAAGGAACAAG
1 GCCACAGAGTTGTGGACTTAAAAGAAAAAGAGTGCCACGGAG-TCGTGGACTTAAAAGGAA-AAG
* * * * * * * *
630944 GGTGCTATGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAGAGT
64 GATGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTCGAGGACTTAAAAGGAAAAAGAGT
* *
631008 GCCACGGAGTTGTGGGCTTAAAAG
1 GCCACAGAGTTGTGGACTTAAAAG
631032 GGTGCCACGA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
126 32 0.25
127 76 0.59
128 21 0.16
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (127 bp):
GCCACAGAGTTGTGGACTTAAAAGAAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAGGA
TGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTCGAGGACTTAAAAGGAAAAAGAGT
Found at i:631051 original size:61 final size:61
Alignment explanation
Indices: 630779--631107 Score: 314
Period size: 61 Copynumber: 5.4 Consensus size: 61
630769 CTTAAAAGGA
* * * *
630779 AAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAATGA-TGCCACGGGGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * * * * * *
630839 AAAAAGGTGCCACGTAGTCGAGGACTTAAAAGGAACAAGAGTGCCACAGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * * * * *
630900 AAAAAGAAAGGGTGCCACGGAGATGTGGACTTAAAAGGAACAAGGGTGCTATGGAGTTGTGGGCT
1 ----A-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
630965 T
61 T
* *
630966 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * * * * * *
631027 AAAAGGGTGCCACGAAGTTATGGACAT-ACAGG-----G-TTGTCACGGAGCTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
*
631081 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
631108 TGAAAAGAGA
Statistics
Matches: 225, Mismatches: 38, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
54 40 0.18
55 1 0.00
60 38 0.17
61 95 0.42
62 1 0.00
65 1 0.00
66 49 0.22
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:631254 original size:33 final size:33
Alignment explanation
Indices: 631139--631530 Score: 493
Period size: 33 Copynumber: 12.2 Consensus size: 33
631129 GAGTTATGGG
* * *
631139 CTTTGAAG--AAAAGATACCACTTAGTCGCGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
* * * *
631170 CTTTG--G-AAAGAGATGCCACTAAGTCATGGG
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
*
631200 CTTTGAAGAAAGAAAGATGCCACTAAGTCGTGGA
1 CTTTGAAGAAA-AAAGATGCCACTGAGTCGTGGA
* *
631234 CTTGGAAGAAAAAAGATGCCACTGAGTCGTGAA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
631267 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
* *
631300 CTTTG--G-AAAGAGATGCCACTGAGTCGTGGG
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
*
631330 CTTTGAAGAAAAAAGATGCCACTGAGTCGTAGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
*
631363 CTTGGAAGAAAAAAGATGCCACTGAGTCGTGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
*
631396 CTTTGAGGAAAAAAGATGCCACTGAGTCGTGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
* * * *
631429 CTTGGAATAAAAAAGATGCCACTCAGTCATGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
631462 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
1 CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
* *
631495 C-TT-AA-AAAAGAA-ATCCCACTGAGTTGTGGA
1 CTTTGAAGAAAA-AAGATGCCACTGAGTCGTGGA
631525 CTTTGA
1 CTTTGA
631531 GAAGAGAGAT
Statistics
Matches: 316, Mismatches: 34, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.00
30 70 0.22
31 12 0.04
32 5 0.02
33 199 0.63
34 29 0.09
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (33 bp):
CTTTGAAGAAAAAAGATGCCACTGAGTCGTGGA
Found at i:631407 original size:129 final size:129
Alignment explanation
Indices: 631147--631531 Score: 555
Period size: 129 Copynumber: 3.0 Consensus size: 129
631137 GGCTTTGAAG
* * *
631147 AAAAGATACCACTTAGTCGCGGACTTTGGAAAGAGATGCCACTAAGTCATGGGCTTTGAAGAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCATGGGCTTTGAAGAAA-
* * *
631212 AAAGATGCCACTAAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGAACTTTGAAGAA
65 AAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGGAA
* *
631277 AAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTGAGTCGTGGGCTTTGAAGAAAA
1 AAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCATGGGCTTTGAAGAAAA
*
631342 AAGATGCCACTGAGTCGTAGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGGAA
66 AAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGGAA
* * *
631406 AAAAGATGCCACTGAGTCGTGGAC-TTGGAATAAAAAAGATGCCACTCAGTCATGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGG----AAAGAGATGCCACTAAGTCATGGGCTTTGAAG
* *
631470 AAAAAAGATGCCACTGAGTCGTGGACTT--AA-AAAAGAA-ATCCCACTGAGTTGTGGACTTTGA
62 AAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAA-AAGATGCCACTGAGTCGTGGACTTTGA
631531 G
126 G
631532 AAGAGAGATT
Statistics
Matches: 234, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
128 4 0.02
129 112 0.48
130 63 0.27
132 55 0.24
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (129 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCATGGGCTTTGAAGAAAA
AAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGGAA
Found at i:633690 original size:13 final size:13
Alignment explanation
Indices: 633672--633697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
633662 CAATTTTTTG
633672 TGTATCGATACAT
1 TGTATCGATACAT
633685 TGTATCGATACAT
1 TGTATCGATACAT
633698 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:636073 original size:21 final size:21
Alignment explanation
Indices: 636049--636095 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
636039 TTTAATGCTG
636049 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
636069 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
636090 ATTTTG
1 ATTTTG
636096 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:636236 original size:13 final size:13
Alignment explanation
Indices: 636218--636256 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
636208 ATAATCACCC
*
636218 TGTATCGATACAG
1 TGTATCGATACAA
636231 TGTATCGATACAA
1 TGTATCGATACAA
636244 TGTATCGATACAA
1 TGTATCGATACAA
636257 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:636267 original size:20 final size:20
Alignment explanation
Indices: 636242--636320 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
636232 GTATCGATAC
636242 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
636262 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
636287 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
636307 CATGTATCGATACA
1 AATGTATCGATACA
636321 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:638357 original size:15 final size:15
Alignment explanation
Indices: 638337--638366 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
638327 ATTTCGTTTG
*
638337 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
638352 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
638367 AGACATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:640199 original size:21 final size:21
Alignment explanation
Indices: 640170--640214 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
640160 AAGTTTTCGT
*
640170 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
640190 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
640212 TTT
1 TTT
640215 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:644071 original size:13 final size:13
Alignment explanation
Indices: 644053--644077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
644043 CATTATGCTT
644053 TGTATCGATACAC
1 TGTATCGATACAC
644066 TGTATCGATACA
1 TGTATCGATACA
644078 TGCTCATTGT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:644090 original size:19 final size:20
Alignment explanation
Indices: 644066--644114 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
644056 ATCGATACAC
*
644066 TGTATCGATACATGCTC-AT
1 TGTATCGATACATACTCAAT
*
644085 TGTATCCATACATACTCAAT
1 TGTATCGATACATACTCAAT
*
644105 TATATCGATA
1 TGTATCGATA
644115 TATGAAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATACTCAAT
Found at i:649007 original size:20 final size:19
Alignment explanation
Indices: 648958--649010 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
648948 CATATCTAGA
**
648958 TGTATCGATACATGTTCAT
1 TGTATCGATACATGCACAT
* *
648977 TGGATCAATACATGCACAAT
1 TGTATCGATACATGCAC-AT
648997 TGTATCGATACATG
1 TGTATCGATACATG
649011 AAACTGGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATGCACAT
Found at i:657808 original size:19 final size:20
Alignment explanation
Indices: 657784--657833 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
657774 TATGCTTTGT
**
657784 ATCGATACATGTTC-ATTGC
1 ATCGATACATGCACAATTGC
*
657803 ATCGATACATGCACAATTGT
1 ATCGATACATGCACAATTGC
657823 ATCGATACATG
1 ATCGATACATG
657834 AAACTAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (20 bp):
ATCGATACATGCACAATTGC
Found at i:657826 original size:20 final size:19
Alignment explanation
Indices: 657780--657833 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
657770 ACATTATGCT
**
657780 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
*
657799 TTGCATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
657819 TTGTATCGATACATG
1 TTGTATCGATACATG
657834 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:661741 original size:20 final size:20
Alignment explanation
Indices: 661712--661764 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
661702 TTAAGTGAAA
* *
661712 TGTATTGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
*
661732 TGTATCGATACCTGAAGAAT
1 TGTATCGATACATGAAGAAT
*
661752 TCTATCGATACAT
1 TGTATCGATACAT
661765 TATGCCCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:669792 original size:24 final size:24
Alignment explanation
Indices: 669761--669809 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
669751 TGAAAAAAAG
669761 ACAAAAAAAATCAAAATCAATTAA
1 ACAAAAAAAATCAAAATCAATTAA
669785 ACAAAAAAAATCAAAATCAATTAA
1 ACAAAAAAAATCAAAATCAATTAA
669809 A
1 A
669810 AAATCAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.16
Consensus pattern (24 bp):
ACAAAAAAAATCAAAATCAATTAA
Found at i:671033 original size:29 final size:29
Alignment explanation
Indices: 670983--671143 Score: 125
Period size: 29 Copynumber: 5.5 Consensus size: 29
670973 AAAGTAACCT
* *
670983 TTTTAAAGTCTATAA-TTCAGTGGCACCCA
1 TTTTAAAGTCCACAACTT-AGTGGCACCCA
*
671012 TTTTAAAGTCCACAACTTAGTGGCACCTCT
1 TTTTAAAGTCCACAACTTAGTGGCACC-CA
** **
671042 TTTTAAAGTCCATGACTTAGTGGCACCTT
1 TTTTAAAGTCCACAACTTAGTGGCACCCA
* *
671071 TTTTAAAGTCCACAGCTCT-GTGGTACCTC-
1 TTTTAAAGTCCACAACT-TAGTGGCACC-CA
*
671100 TTTCTAAAGTCCACAACTTCA-TAGCA-CCA
1 TTT-TAAAGTCCACAACTT-AGTGGCACCCA
*
671129 TTTTCAAAGCCCACA
1 TTTT-AAAGTCCACA
671144 CAAGTAGGTG
Statistics
Matches: 108, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
28 2 0.02
29 61 0.56
30 45 0.42
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (29 bp):
TTTTAAAGTCCACAACTTAGTGGCACCCA
Found at i:671048 original size:30 final size:30
Alignment explanation
Indices: 670981--671118 Score: 158
Period size: 29 Copynumber: 4.7 Consensus size: 30
670971 GTAAAGTAAC
* *
670981 CTTTTTAAAGTCTATAA-TTCAGTGGCACC-
1 CTTTTTAAAGTCCACAACTT-AGTGGCACCT
*
671010 CATTTTAAAGTCCACAACTTAGTGGCACCT
1 CTTTTTAAAGTCCACAACTTAGTGGCACCT
**
671040 CTTTTTAAAGTCCATGACTTAGTGGCACCT
1 CTTTTTAAAGTCCACAACTTAGTGGCACCT
* *
671070 -TTTTTAAAGTCCACAGCTCT-GTGGTACCT
1 CTTTTTAAAGTCCACAACT-TAGTGGCACCT
*
671099 CTTTCTAAAGTCCACAACTT
1 CTTTTTAAAGTCCACAACTT
671119 CATAGCACCA
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
29 47 0.51
30 46 0.49
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (30 bp):
CTTTTTAAAGTCCACAACTTAGTGGCACCT
Found at i:671075 original size:59 final size:59
Alignment explanation
Indices: 670981--671143 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
670971 GTAAAGTAAC
*
670981 CTTTTTAAAGTCTATAATTCAGTGGCACCCATTTTAAAGTCCACAACT-TAGTGGCACCT
1 CTTTTTAAAGTCCATAATTCAGTGGCACCCATTTTAAAGTCCACAACTCT-GTGGCACCT
* ** * *
671040 CTTTTTAAAGTCCATGACTT-AGTGGCACCTTTTTTAAAGTCCACAGCTCTGTGGTACCT
1 CTTTTTAAAGTCCAT-AATTCAGTGGCACCCATTTTAAAGTCCACAACTCTGTGGCACCT
* * * *
671099 CTTTCTAAAGTCCACAACTTCA-TAGCA-CCATTTTCAAAGCCCACA
1 CTTTTTAAAGTCCATAA-TTCAGTGGCACCCATTTT-AAAGTCCACA
671144 CAAGTAGGTG
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
58 6 0.07
59 75 0.87
60 5 0.06
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (59 bp):
CTTTTTAAAGTCCATAATTCAGTGGCACCCATTTTAAAGTCCACAACTCTGTGGCACCT
Found at i:671238 original size:31 final size:33
Alignment explanation
Indices: 671158--671279 Score: 115
Period size: 33 Copynumber: 3.8 Consensus size: 33
671148 TAGGTGGTTT
* *
671158 CCCTTTTCAAAAGTCTACACAAGTTAATGGCAA
1 CCCTTTTCAAAAGCCCACACAAGTTAATGGCAA
**
671191 CCCTTTTCAAAAGCCCACACAAGTTGTTGGCAA
1 CCCTTTTCAAAAGCCCACACAAGTTAATGGCAA
* * *** *
671224 CTC-TTTC-AAAGCCCAAACAAGTCGGTGG-TA
1 CCCTTTTCAAAAGCCCACACAAGTTAATGGCAA
*
671254 TCCTTTCTCAAAAGCCCACACAAGTT
1 CCCTTT-TCAAAAGCCCACACAAGTT
671280 CAAAGTATGC
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.03
31 20 0.27
32 6 0.08
33 45 0.62
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (33 bp):
CCCTTTTCAAAAGCCCACACAAGTTAATGGCAA
Found at i:671551 original size:52 final size:51
Alignment explanation
Indices: 671459--671661 Score: 196
Period size: 52 Copynumber: 3.9 Consensus size: 51
671449 GTTGGCACTC
* * *
671459 TTGTCATATTTAAATCTAAT-TCACTATCCTTGAATCAGCATATTGGTACCT
1 TTGTCATCTTTAAATCCAATATCACTAGCCTTGAATCAGCATATTGG-ACCT
* * * * * *
671510 TTATTATCTTTAGATCTAATATCACTAGCCTTGAATAAGCATATT-GACAT
1 TTGTCATCTTTAAATCCAATATCACTAGCCTTGAATCAGCATATTGGACCT
* * *
671560 ACTTGTCAT-TTGTAAATCCAATATCGCTAGCCTTGAACCATCATATTGGCACCT
1 --TTGTCATCTT-TAAATCCAATATCACTAGCCTTGAATCAGCATATTGG-ACCT
* * *
671614 TCGTCATCTTTAAGATCCAATATCGCTAGCCTTGAATCAGTATATTGG
1 TTGTCATCTTTAA-ATCCAATATCACTAGCCTTGAATCAGCATATTGG
671662 CACTTTAATC
Statistics
Matches: 124, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
50 3 0.02
51 19 0.15
52 65 0.52
53 34 0.27
54 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (51 bp):
TTGTCATCTTTAAATCCAATATCACTAGCCTTGAATCAGCATATTGGACCT
Done.