Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 6 of 24
Found at i:754519 original size:32 final size:31
Alignment explanation
Indices: 754473--754533 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
754463 AATATATTAT
* * *
754473 TTAAAAATAAATGAAAATTAAAAACTAAAAA
1 TTAAAAAAAAATGAAAACTAAAAAATAAAAA
754504 TTAAATAAAAAATGAAAACTAAAAAATAAA
1 TTAAA-AAAAAATGAAAACTAAAAAATAAA
754534 GCTTTGCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (31 bp):
TTAAAAAAAAATGAAAACTAAAAAATAAAAA
Found at i:756792 original size:24 final size:23
Alignment explanation
Indices: 756755--756812 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
756745 TAATAATAAA
756755 TTTTT-TA-TTTTAAAAT-TATT
1 TTTTTATATTTTTAAAATATATT
756775 TTTATTAATATTTTTAAAATATATT
1 TTT-TT-ATATTTTTAAAATATATT
756800 TTTTTATATTTTT
1 TTTTTATATTTTT
756813 GTTAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
23 10 0.30
24 11 0.33
25 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTATATTTTTAAAATATATT
Found at i:756798 original size:13 final size:13
Alignment explanation
Indices: 756762--756802 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
756752 AAATTTTTTA
756762 TTTTAAAAT-TAT
1 TTTTAAAATATAT
**
756774 TTTTATTA-ATAT
1 TTTTAAAATATAT
756786 TTTTAAAATATAT
1 TTTTAAAATATAT
756799 TTTT
1 TTTT
756803 TTATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:757552 original size:74 final size:73
Alignment explanation
Indices: 757416--757601 Score: 179
Period size: 73 Copynumber: 2.6 Consensus size: 73
757406 TATATGTATT
* * * * *
757416 TAAATT-TTATAAGATAT-AATT-TTTTTATTTATATATATTTTAATTTAATTTTTTGTTTGATT
1 TAAATTATTGTAAGATATGATTTATTTTTATTTGTA-AAATTTTAATTTAATTTTTAGTTTGATT
*
757478 ATATAAGT-
65 ATAGAAGTA
* * *
757486 TAAAATTTTTTTTAACG-TATGATTTATTTTTATTTGTAGAATTTTAAATTT-ATTTTTAAG-TT
1 T-AAA-TTATTGTAA-GATATGATTTATTTTTATTTGTAAAATTTT-AATTTAATTTTT-AGTTT
*
757548 GATTATAGGAGTA
61 GATTATAGAAGTA
757561 TAAATTATTGTAAGATATGATTTATTTTTATTTGTAAAATT
1 TAAATTATTGTAAGATATGATTTATTTTTATTTGTAAAATT
757602 AGTTTGATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
70 1 0.01
71 3 0.03
72 3 0.03
73 40 0.42
74 30 0.32
75 18 0.19
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (73 bp):
TAAATTATTGTAAGATATGATTTATTTTTATTTGTAAAATTTTAATTTAATTTTTAGTTTGATTA
TAGAAGTA
Found at i:757833 original size:68 final size:68
Alignment explanation
Indices: 757751--757882 Score: 214
Period size: 68 Copynumber: 1.9 Consensus size: 68
757741 ACGAGTTTAA
*
757751 ATTTTTAAGATATAATTTATTTTTATTTGA-AAAAATTTAAATTTGTATTTCGATTTGATTATAA
1 ATTTTTAAGATATAATTTATTTTTATTT-ATAAAAATTTAAATTTATATTTCGATTTGATTATAA
757815 GAGT
65 GAGT
*
757819 ATTTTTAATG-TATAATTTATTTTTATTTATAAAAATTTAAATTTATATTTTGATTTGATTATAA
1 ATTTTTAA-GATATAATTTATTTTTATTTATAAAAATTTAAATTTATATTTCGATTTGATTATAA
757883 AAATTTAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
67 1 0.02
68 58 0.97
69 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.55
Consensus pattern (68 bp):
ATTTTTAAGATATAATTTATTTTTATTTATAAAAATTTAAATTTATATTTCGATTTGATTATAAG
AGT
Found at i:757881 original size:32 final size:32
Alignment explanation
Indices: 757781--757894 Score: 113
Period size: 32 Copynumber: 3.4 Consensus size: 32
757771 TTTTATTTGA
* *
757781 AAAAATTTAAATTTGTATTTCGATTTGATTAT
1 AAAAATTTAAATTTATATTTTGATTTGATTAT
* * * * *
757813 AAGAGTATTTTTAATGTATAATTT-ATTTTTATTTAT
1 AA-A--AATTTAAATTTATATTTTGA-TTTGA-TTAT
757849 AAAAATTTAAATTTATATTTTGATTTGATTAT
1 AAAAATTTAAATTTATATTTTGATTTGATTAT
757881 AAAAATTTAAATTT
1 AAAAATTTAAATTT
757895 TTAAAATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
32 20 0.31
33 19 0.30
34 2 0.03
35 17 0.27
36 6 0.09
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (32 bp):
AAAAATTTAAATTTATATTTTGATTTGATTAT
Found at i:757907 original size:68 final size:70
Alignment explanation
Indices: 757746--757910 Score: 180
Period size: 68 Copynumber: 2.4 Consensus size: 70
757736 ATTATACGAG
*
757746 TTTAAATTTTTAAGATATAATTTATTTTTATTTGAAAAAATTTAAATTTGTATTTCGATTTGATT
1 TTTAAATTTTTAA-A-AT-A-TTATTTTTATTTGAAAAAATTTAAATTTATATTTCGATTTGATT
*
757811 ATAAGAGTAT
62 ATAAGAG-AA
* * * *
757821 TTTTAA--TGTATAAT-TTATTTTTATTT-ATAAAAATTTAAATTTATATTTTGATTTGATTATA
1 TTTAAATTTTTAAAATATTATTTTTATTTGA-AAAAATTTAAATTTATATTTCGATTTGATTATA
757882 A-A-AA
65 AGAGAA
757886 TTTAAATTTTTAAAATATTATTTTT
1 TTTAAATTTTTAAAATATTATTTTT
757911 TTGTAAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
65 6 0.08
67 8 0.10
68 52 0.68
71 2 0.03
72 1 0.01
73 3 0.04
75 5 0.06
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (70 bp):
TTTAAATTTTTAAAATATTATTTTTATTTGAAAAAATTTAAATTTATATTTCGATTTGATTATAA
GAGAA
Found at i:757922 original size:17 final size:19
Alignment explanation
Indices: 757892--757935 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
757882 AAAATTTAAA
757892 TTTT-TAAAATATTA-TTT
1 TTTTGTAAAATATTATTTT
757909 TTTTGTAAAA-ATTATTTT
1 TTTTGTAAAATATTATTTT
757927 TTTTGTAAA
1 TTTTGTAAA
757936 GAGCTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTGTAAAATATTATTTT
Found at i:758383 original size:13 final size:14
Alignment explanation
Indices: 758382--758426 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
758372 TTTAAAAAAT
758382 AAAAATATATTTTA
1 AAAAATATATTTTA
**
758396 AAAAATAT-TAATA
1 AAAAATATATTTTA
*
758409 AAAAATATAATTTA
1 AAAAATATATTTTA
758423 AAAA
1 AAAA
758427 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATATATTTTA
Found at i:758386 original size:21 final size:20
Alignment explanation
Indices: 758362--758402 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
758352 TTATTGTTTC
758362 AAAAGATAATTTTAAAAAATA
1 AAAAGAT-ATTTTAAAAAATA
*
758383 AAAATATATTTTAAAAAATA
1 AAAAGATATTTTAAAAAATA
758403 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAGATATTTTAAAAAATA
Found at i:758427 original size:13 final size:13
Alignment explanation
Indices: 758381--758428 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
758371 TTTTAAAAAA
*
758381 TAAAAATATATTT
1 TAAAAATATAATT
758394 TAAAAAATATTAA-T
1 T-AAAAATA-TAATT
*
758408 AAAAAATATAATT
1 TAAAAATATAATT
758421 TAAAAATA
1 TAAAAATA
758429 AAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.10
13 16 0.55
14 8 0.28
15 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAATATAATT
Found at i:758435 original size:27 final size:27
Alignment explanation
Indices: 758374--758435 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
758364 AAGATAATTT
*
758374 TAAAAAAT-AAAAATATATTTTAAAAA
1 TAAAAAATAAAAAATATAATTTAAAAA
**
758400 -ATATTAATAAAAAATATAATTTAAAAA
1 TA-AAAAATAAAAAATATAATTTAAAAA
758427 TAAAAAATA
1 TAAAAAATA
758436 TTATTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.04
26 4 0.14
27 22 0.79
28 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAAAAATAAAAAATATAATTTAAAAA
Found at i:762069 original size:9 final size:9
Alignment explanation
Indices: 762055--762092 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
762045 ATCGATCAAT
762055 TTTTTTTAA
1 TTTTTTTAA
762064 TTTTTTTAA
1 TTTTTTTAA
*
762073 TTACTTTT-A
1 TT-TTTTTAA
762082 TTTTTTTAA
1 TTTTTTTAA
762091 TT
1 TT
762093 CAAATTCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:762160 original size:17 final size:17
Alignment explanation
Indices: 762125--762160 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
762115 GAACCAAGTA
* *
762125 TTATTTTTTTATTTTTT
1 TTATTTTTTTAGTTGTT
762142 TTATTTTTTTAGTTGTT
1 TTATTTTTTTAGTTGTT
762159 TT
1 TT
762161 TGTTAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (17 bp):
TTATTTTTTTAGTTGTT
Found at i:762511 original size:21 final size:20
Alignment explanation
Indices: 762475--762525 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
762465 TAAACTTAAC
* * *
762475 TTTTAAATTTAATTTATATT
1 TTTTAAATATAATTTAAATA
*
762495 TTATTAAATATATTTTAAATA
1 TT-TTAAATATAATTTAAATA
762516 TTTTAAATAT
1 TTTTAAATAT
762526 TAAATTCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATATAATTTAAATA
Found at i:767124 original size:100 final size:100
Alignment explanation
Indices: 766947--767149 Score: 282
Period size: 100 Copynumber: 2.0 Consensus size: 100
766937 TGTACTTAAT
* *
766947 TTTTTTGATCATGGCTAGTAAGGTATAAATTTTTATGCTTAAAATTCAACAATGACTCCAGTAGT
1 TTTTTTGATCATGGCTAGTAAGCTATAAATTCTTATGCTTAAAATTCAACAATGACTCCAGTAGT
* * *
767012 TGCCTTCAACTTCTATTAGCTAGTTCTTCCTGGTG
66 TGCCTTCAACTTCTATGACCAAGTTCTTCCTGGTG
* * * * *
767047 TTTTTTGGTCATGGTTGGTAAGCTATAAATTCTTATGCTTAAAATTCCAGAATGACTCCAGT-GA
1 TTTTTTGATCATGGCTAGTAAGCTATAAATTCTTATGCTTAAAATTCAACAATGACTCCAGTAG-
**
767111 TTGCCTTTGACTTCTATGACCAAGTTCTTCCTGGTG
65 TTGCCTTCAACTTCTATGACCAAGTTCTTCCTGGTG
767147 TTT
1 TTT
767150 ACTTCAATCT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
99 1 0.01
100 89 0.99
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (100 bp):
TTTTTTGATCATGGCTAGTAAGCTATAAATTCTTATGCTTAAAATTCAACAATGACTCCAGTAGT
TGCCTTCAACTTCTATGACCAAGTTCTTCCTGGTG
Found at i:769880 original size:25 final size:25
Alignment explanation
Indices: 769830--769886 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
769820 CATTTAAATG
* * *
769830 AATACAACGTAAATAAATTTATTAA
1 AATATAACATAAATAAATATATTAA
769855 AATATAACATAAATAAATA-ATATAA
1 AATATAACATAAATAAATATAT-TAA
769880 ATATATA
1 A-ATATA
769887 CAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (25 bp):
AATATAACATAAATAAATATATTAA
Found at i:770606 original size:34 final size:33
Alignment explanation
Indices: 770558--770778 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
770548 TGGTAAAAAC
* *
770558 CACCATTTAATCAACAATGGCAATCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* *
770591 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
770625 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
**
770659 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
770693 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
770727 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
770761 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
770779 TCTCCCACTT
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
33 19 0.12
34 143 0.88
35 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:770702 original size:102 final size:101
Alignment explanation
Indices: 770558--770778 Score: 352
Period size: 102 Copynumber: 2.2 Consensus size: 101
770548 TGGTAAAAAC
* * *
770558 CACCATTTAATCAACAATGGCAATCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
770623 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
770659 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
770724 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
770761 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
770779 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:775232 original size:34 final size:33
Alignment explanation
Indices: 775184--775403 Score: 242
Period size: 34 Copynumber: 6.5 Consensus size: 33
775174 TGGTAAAAAC
*
775184 CACCATTTAATCAACAATGGTAATCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* *
775217 CTACCATTTAGTCAACAATGGTAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
* * *
775251 CACCCATTTAATCAATAATGATAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
** *
775285 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
* * * * **
775319 CTCCCATTTAGTTAACAATGGTAAACCATTAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
*
775353 CACCCATTTAATCAACAATGATAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
*
775387 CACCATTTAATTAACAA
1 CACCATTTAATCAACAA
775404 GGGCAAGCCT
Statistics
Matches: 154, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
33 17 0.11
34 136 0.88
35 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:775363 original size:102 final size:101
Alignment explanation
Indices: 775184--775403 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
775174 TGGTAAAAAC
*
775184 CACCATTTAATCAACAATGGTAATCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGTAAGCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
* *
775249 ATCACCCATTTAATCAATAATGATAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * * **
775285 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGTAAACCATTA
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCA
775350 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
*
775387 CACCATTTAATTAACAA
1 CACCATTTAATCAACAA
775404 GGGCAAGCCT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 92 0.87
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:778335 original size:13 final size:13
Alignment explanation
Indices: 778317--778341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
778307 TCAAACGATT
778317 TGTATCGATACAA
1 TGTATCGATACAA
778330 TGTATCGATACA
1 TGTATCGATACA
778342 TAAGTGTTGT
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:778354 original size:19 final size:19
Alignment explanation
Indices: 778330--778379 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
778320 ATCGATACAA
778330 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
778349 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
778368 TGTATCGATACA
1 TGTATCGATACA
778380 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:778450 original size:13 final size:13
Alignment explanation
Indices: 778432--778456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
778422 ATTACTCAAA
778432 TGTATCGATACAT
1 TGTATCGATACAT
778445 TGTATCGATACA
1 TGTATCGATACA
778457 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:778509 original size:52 final size:52
Alignment explanation
Indices: 778465--778593 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
778455 CACTGATCTT
778465 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
* * *
778517 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
*
778569 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
778594 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
Found at i:779634 original size:13 final size:13
Alignment explanation
Indices: 779616--779641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
779606 TACACCAAGT
779616 ATGTATCGATACA
1 ATGTATCGATACA
779629 ATGTATCGATACA
1 ATGTATCGATACA
779642 CAAAAAATTG
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:779639 original size:32 final size:33
Alignment explanation
Indices: 779598--779661 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
779588 TAGCCAAACT
* **
779598 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
779630 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
779662 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:783716 original size:15 final size:15
Alignment explanation
Indices: 783696--783726 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
783686 TAAAAATGTC
*
783696 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
783711 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
783726 C
1 C
783727 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:785805 original size:13 final size:13
Alignment explanation
Indices: 785787--785825 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
785777 ACATTTTTCT
785787 TTGTATCGATACA
1 TTGTATCGATACA
785800 TTGTATCGATACA
1 TTGTATCGATACA
*
785813 CTGTATCGATACA
1 TTGTATCGATACA
785826 GGGGATTATA
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:786293 original size:20 final size:21
Alignment explanation
Indices: 786268--786308 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
786258 AGCACCACCT
*
786268 AGGTCGCGACC-GGCACTCCC
1 AGGTCGCAACCAGGCACTCCC
*
786288 AGGTCGCAACCAGGCAGTCCC
1 AGGTCGCAACCAGGCACTCCC
786309 CACACTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.41, G:0.29, T:0.10
Consensus pattern (21 bp):
AGGTCGCAACCAGGCACTCCC
Found at i:788389 original size:13 final size:13
Alignment explanation
Indices: 788371--788396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
788361 TACACCAAGT
788371 ATGTATCGATACA
1 ATGTATCGATACA
788384 ATGTATCGATACA
1 ATGTATCGATACA
788397 CAAAAAATTG
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:788394 original size:32 final size:33
Alignment explanation
Indices: 788353--788416 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
788343 TAGCCAAACT
* **
788353 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
788385 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
788417 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:790548 original size:26 final size:26
Alignment explanation
Indices: 790519--790600 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
790509 AATTACAATT
790519 AAATTGCAAATATTGAAACCGAATAA
1 AAATTGCAAATATTGAAACCGAATAA
* * * *
790545 AAATT-TAAAT-TTAAAAATTAC-AAT-T
1 AAATTGCAAATATT-GAAA--CCGAATAA
*
790570 AAATTGCAAATATTGAAACTGAATAA
1 AAATTGCAAATATTGAAACCGAATAA
790596 AAATT
1 AAATT
790601 AAAATTTAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
24 2 0.05
25 15 0.38
26 20 0.50
27 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (26 bp):
AAATTGCAAATATTGAAACCGAATAA
Found at i:790566 original size:51 final size:51
Alignment explanation
Indices: 790509--790609 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
790499 TTATTTTGGG
*
790509 AATTACAATTAAATTGCAAATATTGAAACCGAATAAAAATTTAAATTTAAA
1 AATTACAATTAAATTGCAAATATTGAAACCGAATAAAAATTAAAATTTAAA
*
790560 AATTACAATTAAATTGCAAATATTGAAACTGAATAAAAATTAAAATTTAA
1 AATTACAATTAAATTGCAAATATTGAAACCGAATAAAAATTAAAATTTAA
790610 GTTAACATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (51 bp):
AATTACAATTAAATTGCAAATATTGAAACCGAATAAAAATTAAAATTTAAA
Found at i:794756 original size:13 final size:14
Alignment explanation
Indices: 794738--794786 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
794728 TCCTAGTTTT
794738 TCTTTTT-TTTCTC
1 TCTTTTTCTTTCTC
794751 TCTTTTTC-TT-TC
1 TCTTTTTCTTTCTC
*
794763 T-TTTTTCTCTC-C
1 TCTTTTTCTTTCTC
794775 TCTTTTTCTTTC
1 TCTTTTTCTTTC
794787 AGCTGAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 6 0.20
12 6 0.20
13 18 0.60
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTTTTTCTTTCTC
Found at i:794762 original size:23 final size:24
Alignment explanation
Indices: 794736--794786 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
794726 TTTCCTAGTT
*
794736 TTTCTTTTTTTTCT-CTCTTTTTC
1 TTTCTTTTTTCTCTCCTCTTTTTC
794759 TTTCTTTTTTCTCTCCTCTTTTTC
1 TTTCTTTTTTCTCTCCTCTTTTTC
794783 TTTC
1 TTTC
794787 AGCTGAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTCTTTTTTCTCTCCTCTTTTTC
Found at i:794773 original size:21 final size:19
Alignment explanation
Indices: 794734--794772 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
794724 ATTTTCCTAG
794734 TTTTTCTTTTTTTTCTCTC
1 TTTTTCTTTTTTTTCTCTC
794753 TTTTTCTTTCTTTTT-TCTC
1 TTTTTCTTT-TTTTTCTCTC
794772 T
1 T
794773 CCTCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTCTC
Found at i:798054 original size:19 final size:19
Alignment explanation
Indices: 798030--798068 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
798020 GGTGGAATAA
798030 AATGATCTTTGATCTAATC
1 AATGATCTTTGATCTAATC
798049 AATGATCTTTGATCTAATC
1 AATGATCTTTGATCTAATC
798068 A
1 A
798069 CATTTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (19 bp):
AATGATCTTTGATCTAATC
Found at i:799593 original size:33 final size:32
Alignment explanation
Indices: 799551--799614 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
799541 TACAAGCTAA
**
799551 TGTATCGATACATTTTTTGGTGTATCCATACAT
1 TGTATCGATACATACTTT-GTGTATCCATACAT
*
799584 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCCATACA
799615 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCCATACAT
Found at i:800262 original size:20 final size:22
Alignment explanation
Indices: 800237--800277 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
800227 TTCTTTTCTT
800237 TCCCCC-TAA-AAAATAATTTC
1 TCCCCCTTAATAAAATAATTTC
*
800257 TCCCCCTTAATAAGATAATTT
1 TCCCCCTTAATAAAATAATTT
800278 TAACAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (22 bp):
TCCCCCTTAATAAAATAATTTC
Found at i:801101 original size:21 final size:20
Alignment explanation
Indices: 801055--801101 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
801045 TTTGAAGCTG
*
801055 ATTTTGATGAAAAACGATGT
1 ATTTTGATGAAAAACGAAGT
*
801075 AATTTGAAGTGAAAAAC-AAGT
1 ATTTTG-A-TGAAAAACGAAGT
801096 ATTTTG
1 ATTTTG
801102 CAAAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:801241 original size:13 final size:13
Alignment explanation
Indices: 801225--801261 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
801215 AATCCTCCTA
* *
801225 TATCAATACAGTG
1 TATCGATACAATG
801238 TATCGATACAATG
1 TATCGATACAATG
801251 TATCGATACAA
1 TATCGATACAA
801262 AGAATGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:803898 original size:33 final size:33
Alignment explanation
Indices: 803861--803927 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
803851 TTCAACGATT
803861 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
803894 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
803927 T
1 T
803928 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:803899 original size:13 final size:13
Alignment explanation
Indices: 803881--803905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
803871 CATAAAATGT
803881 TGTATCGATACAA
1 TGTATCGATACAA
803894 TGTATCGATACA
1 TGTATCGATACA
803906 TATTTTTTTG
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:803988 original size:13 final size:13
Alignment explanation
Indices: 803970--803994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
803960 ATTACTCACA
803970 TGTATCGATACAT
1 TGTATCGATACAT
803983 TGTATCGATACA
1 TGTATCGATACA
803995 CTAATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:804059 original size:52 final size:52
Alignment explanation
Indices: 804003--804127 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
803993 CACTAATCTT
*
804003 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
804055 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
804107 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
804128 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:806282 original size:24 final size:26
Alignment explanation
Indices: 806255--806306 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
806245 TATCAAAATT
*
806255 CATTCAT-C-GGGGATACTCCAACCC
1 CATTCATCCAGGGGACACTCCAACCC
*
806279 CATTCCTCCGAGGGGACACTCCAACCC
1 CATTCATCC-AGGGGACACTCCAACCC
806306 C
1 C
806307 GTTTTCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.17
Consensus pattern (26 bp):
CATTCATCCAGGGGACACTCCAACCC
Found at i:810344 original size:32 final size:33
Alignment explanation
Indices: 810284--810347 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
810274 TACAAGCTAA
**
810284 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
*
810317 TGTATTGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
810348 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:812553 original size:142 final size:143
Alignment explanation
Indices: 812223--812561 Score: 375
Period size: 142 Copynumber: 2.4 Consensus size: 143
812213 AGGAGATATA
* ** ** * * *
812223 AAAAGTTT-TAAATATTTCTATA-CTCCTATAGAAAACCATAGGAATATTAGAAATCTTGAAAAT
1 AAAAGTTTCGAAA-ATTTCTATACCT-CTACGGAAAACCATAAAAATATTAGAAATATAGAAAAA
** *
812286 TTAAGATAATAATTTTTATTTGATTTTTTCAATTTTTAAAAAATTCATTTCGTACCTTAATGGAG
64 TTAAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAG
* * *
812351 GACTGAAACGATACG
129 AACCGAAAAGATACG
* * *
812366 AAAAGTTTCGAAGATTTCTATACCTTTACGGAAAACCATAAAAATATTAAAAATATAGAAAAATT
1 AAAAGTTTCGAAAATTTCTATACCTCTACGGAAAACCATAAAAATATTAGAAATATAGAAAAATT
*
812431 AAGATAATAATTTTTATTCAATTTTTT-AATTTCTAAAAAATTCATTTTGTACCTTAATGGAGAA
66 AAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAA
*
812495 CCGAAAAGATA-T
131 CCGAAAAGATACG
* * * **
812507 AAAATGTTTTGAAAATTT-TCATACCTCTATGG-ATACCTATGGAAATATTAGAAAT
1 AAAA-GTTTCGAAAATTTCT-ATACCTCTACGGAAAACC-ATAAAAATATTAGAAAT
812562 TCCAAAAAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
141 9 0.05
142 78 0.48
143 73 0.45
144 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (143 bp):
AAAAGTTTCGAAAATTTCTATACCTCTACGGAAAACCATAAAAATATTAGAAATATAGAAAAATT
AAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAA
CCGAAAAGATACG
Found at i:812570 original size:142 final size:143
Alignment explanation
Indices: 812223--812535 Score: 375
Period size: 143 Copynumber: 2.2 Consensus size: 143
812213 AGGAGATATA
* ** ** * * * *
812223 AAAAGTTT-TAAATATTTCTATA-CTCCTATAGAAAACCATAGGAATATTAGAAATCTTGAAAAT
1 AAAAGTTTCGAAA-ATTTCTATACCT-CTACGGAAAACCATAAAAATATTAAAAATATAGAAAAA
** *
812286 TTAAGATAATAATTTTTATTTGATTTTTTCAATTTTTAAAAAATTCATTTCGTACCTTAATGGAG
64 TTAAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAG
* * *
812351 GACTGAAACGATACG
129 AACCGAAAAGATACG
* *
812366 AAAAGTTTCGAAGATTTCTATACCTTTACGGAAAACCATAAAAATATTAAAAATATAGAAAAATT
1 AAAAGTTTCGAAAATTTCTATACCTCTACGGAAAACCATAAAAATATTAAAAATATAGAAAAATT
*
812431 AAGATAATAATTTTTATTCAATTTTTT-AATTTCTAAAAAATTCATTTTGTACCTTAATGGAGAA
66 AAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAA
*
812495 CCGAAAAGATA-T
131 CCGAAAAGATACG
*
812507 AAAATGTTTTGAAAATTT-TCATACCTCTA
1 AAAA-GTTTCGAAAATTTCT-ATACCTCTA
812536 TGGATACCTA
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
141 5 0.03
142 62 0.43
143 73 0.51
144 4 0.03
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (143 bp):
AAAAGTTTCGAAAATTTCTATACCTCTACGGAAAACCATAAAAATATTAAAAATATAGAAAAATT
AAGATAATAATTTTTATTCAATTTTTTCAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAA
CCGAAAAGATACG
Found at i:813538 original size:30 final size:29
Alignment explanation
Indices: 813487--813544 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
813477 ACTAATTTTC
813487 TTTTTTTTCCTTTTTCTTCTCTTCTCTTT
1 TTTTTTTTCCTTTTTCTTCTCTTCTCTTT
*
813516 TTTTTTTCTCTCTTTTTC-TCTCTTTTCTT
1 TTTTTTT-TC-CTTTTTCTTCTCTTCTCTT
813545 CTCACTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 12 0.46
31 7 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTTTTTTCCTTTTTCTTCTCTTCTCTTT
Found at i:815664 original size:85 final size:85
Alignment explanation
Indices: 815560--815935 Score: 470
Period size: 85 Copynumber: 4.4 Consensus size: 85
815550 GGACTAAATT
815560 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAA
1 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAA
*
815625 GA-TGTGACTAGGATTGAACC
66 GAGT-TGACTGGGATTGAACC
* * * ** * *
815645 GATAAGTCAATAAAAGATAAAAAGATTTACTCGGGACTAAATCGACAGGTAAATAAAGGATGAAA
1 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAA
**
815710 GAGTTGACTGGGATTGAATT
66 GAGTTGACTGGGATTGAACC
* * * *
815730 GACAAGTCAACAAAGGATAAAAAGATTTACCCGAGACTAAGCCAACAGGTAAATAAGGGATGCAA
1 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATG-AA
* *
815795 A-AGTTGACTGGGACTGAATC
65 AGAGTTGACTGGGATTGAACC
* * * * * *
815815 AATAAGTCAACAAAAGATAAAAATATTTCCTCGGGACTAAGCCAACAGGTAAACAAAGGA-CAAA
1 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAA
* **
815879 AAGGTTGACTGAAATTGAACC
66 GA-GTTGACTGGGATTGAACC
*
815900 GATAAGTCAACAAAGGATAAAAGGATTTACTCGAGA
1 GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGA
815936 ATAGTTGATA
Statistics
Matches: 246, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
83 3 0.01
84 1 0.00
85 238 0.97
86 4 0.02
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (85 bp):
GATAAGTCAACAAAGGATAAAAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAA
GAGTTGACTGGGATTGAACC
Found at i:815746 original size:42 final size:42
Alignment explanation
Indices: 815611--815747 Score: 116
Period size: 42 Copynumber: 3.2 Consensus size: 42
815601 CCAACAGGTA
* * *
815611 AACAAAGGATGAAAGA-TGTGACTAGGATTGAACCGATAAGTC
1 AACAAAGGATGAAAGAGT-TGACTGGGATTGAATCGACAAGTC
* * * * * * * *
815653 AATAAAAGAT-AAAAAGATTTACTCGGGACTAAATCGACAGGTA
1 AACAAAGGATGAAAGAG-TTGACT-GGGATTGAATCGACAAGTC
* *
815696 AATAAAGGATGAAAGAGTTGACTGGGATTGAATTGACAAGTC
1 AACAAAGGATGAAAGAGTTGACTGGGATTGAATCGACAAGTC
815738 AACAAAGGAT
1 AACAAAGGAT
815748 AAAAAGATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
41 4 0.06
42 35 0.49
43 27 0.38
44 5 0.07
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.20
Consensus pattern (42 bp):
AACAAAGGATGAAAGAGTTGACTGGGATTGAATCGACAAGTC
Found at i:815753 original size:170 final size:170
Alignment explanation
Indices: 815517--815935 Score: 533
Period size: 170 Copynumber: 2.5 Consensus size: 170
815507 GTTACTTGAG
* * * *
815517 CCGACATGTAGATAAAGGATACAAAGA-TTGACT-GGACTAAATTGATAAGTCAACAAAGGATAA
1 CCGACAGGTAAATAAAGGAT-CAAAGAGTTGACTGGGATTGAATTGATAAGTCAACAAAGGATAA
*
815580 AAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATG--AAAGATGTGACTAGGATTGAA
65 AAAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGCAAAAG-T-TGACTAGGACTGAA
* *
815643 CCGATAAGTCAATAAAAGATAAAAAGATTTACTCGGGACTAAA
128 CCAATAAGTCAACAAAAGATAAAAAGATTTACTCGGGACTAAA
* * *
815686 TCGACAGGTAAATAAAGGATGAAAGAGTTGACTGGGATTGAATTGACAAGTCAACAAAGGATAAA
1 CCGACAGGTAAATAAAGGATCAAAGAGTTGACTGGGATTGAATTGATAAGTCAACAAAGGATAAA
* * * * *
815751 AAGATTTACCCGAGACTAAGCCAACAGGTAAATAAGGGATGCAAAAGTTGACTGGGACTGAATCA
66 AAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGCAAAAGTTGACTAGGACTGAACCA
* * *
815816 ATAAGTCAACAAAAGATAAAAATATTTCCTCGGGACTAAG
131 ATAAGTCAACAAAAGATAAAAAGATTTACTCGGGACTAAA
* * * ** **
815856 CCAACAGGTAAACAAAGGA-CAAAAAGGTTGACTGAAATTGAACCGATAAGTCAACAAAGGATAA
1 CCGACAGGTAAATAAAGGATCAAAGA-GTTGACTGGGATTGAATTGATAAGTCAACAAAGGATAA
*
815920 AAGGATTTACTCGAGA
65 AAAGATTTACTCGAGA
815936 ATAGTTGATA
Statistics
Matches: 215, Mismatches: 30, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
168 5 0.02
169 27 0.13
170 178 0.83
171 1 0.00
172 4 0.02
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (170 bp):
CCGACAGGTAAATAAAGGATCAAAGAGTTGACTGGGATTGAATTGATAAGTCAACAAAGGATAAA
AAGATTTACTCGAGACTAAGCCAACAGGTAAACAAAGGATGCAAAAGTTGACTAGGACTGAACCA
ATAAGTCAACAAAAGATAAAAAGATTTACTCGGGACTAAA
Found at i:816257 original size:47 final size:48
Alignment explanation
Indices: 816173--816279 Score: 130
Period size: 47 Copynumber: 2.2 Consensus size: 48
816163 ACTAGAATGG
* * *
816173 AAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACT-AGGGTGAA
1 AAAAAGTTTGACTAGGTCCTAATGCCAATACAATCAAA-TGAAGGTGAA
*
816221 AAAAAGTTTGA-TAGGTCCTAATTG-TAATACAATCAAATGAAGGTGAA
1 AAAAAGTTTGACTAGGTCCTAA-TGCCAATACAATCAAATGAAGGTGAA
*
816268 AAATAGTTTGAC
1 AAAAAGTTTGAC
816280 CAAGACTAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
46 1 0.02
47 37 0.73
48 13 0.25
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (48 bp):
AAAAAGTTTGACTAGGTCCTAATGCCAATACAATCAAATGAAGGTGAA
Found at i:817419 original size:30 final size:30
Alignment explanation
Indices: 817383--817453 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
817373 ATAGGACATG
817383 TATCGATACATTCTATTTTTTACCTAGATA
1 TATCGATACATTCTATTTTTTACCTAGATA
* *
817413 TATCGATACATTCTGTTTTTTACCTAGATG
1 TATCGATACATTCTATTTTTTACCTAGATA
*
817443 TATCAATACAT
1 TATCGATACAT
817454 GTATGAATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (30 bp):
TATCGATACATTCTATTTTTTACCTAGATA
Found at i:817482 original size:20 final size:20
Alignment explanation
Indices: 817440--817490 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
817430 TTTTACCTAG
* *
817440 ATGTATCAATACATGTATGA
1 ATGTATCGATACATGTATCA
* *
817460 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
817480 ATGTATCGATA
1 ATGTATCGATA
817491 TATTCTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:818347 original size:299 final size:299
Alignment explanation
Indices: 817809--818709 Score: 1757
Period size: 299 Copynumber: 3.0 Consensus size: 299
817799 TATCAGCTAA
* *
817809 ACAACATCATGTTGTCAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAATACCTCC
1 ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
817874 TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
66 TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
817939 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
131 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
*
818004 AAGGAAGAAATGCTCAACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
196 AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
818069 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
261 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
818108 ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
1 ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
*
818173 TATTTGACACCAATATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
66 TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
818238 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
131 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
818303 AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
196 AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
818368 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
261 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
818407 ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
1 ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
818472 TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
66 TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
818537 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
131 GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
818602 AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
196 AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
*
818667 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTCACT
261 TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
818706 ACAA
1 ACAA
818710 GAATTGATTA
Statistics
Matches: 596, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 596 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (299 bp):
ACAACATCATGTTGTTAGCACCTTGTCTTGCAAATTGGTTGAGGGAAATGACCCAAAACACCTCC
TATTTGACACCAACATTTTGGCTATTGAAAGCTCAAGGAATAATGAACCAAGAGGGGGTTAATTG
GTTCTTTTCGAATTTTGAGTGTTTTGAAAGATTTGGTACAAAACAATTCCAAAGATAAAAAGATT
AAGGAAGAAATGCTCGACACCAGAGTTTATAGAGGTTCGGTCTAATTCAGTACCTACATCCTCTC
TCTTCGACACTTCTTCGTCGAGTGGTTATCCAATTTACT
Found at i:819377 original size:19 final size:20
Alignment explanation
Indices: 819329--819384 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
819319 CTGCCAGTTT
*
819329 CATGTATCGATACAATTATA
1 CATGTATCGATACAATGATA
819349 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
819368 CA-GTTATCGATACAATG
1 CATG-TATCGATACAATG
819385 TATTGATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 17 0.50
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:821059 original size:13 final size:14
Alignment explanation
Indices: 821030--821057 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
821020 TGTGCATTCA
821030 TGTTTACAAAAATT
1 TGTTTACAAAAATT
821044 TGTTTACAAAAATT
1 TGTTTACAAAAATT
821058 GTAGAGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTTTACAAAAATT
Found at i:825521 original size:18 final size:17
Alignment explanation
Indices: 825498--825534 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
825488 GAAAAAAGCC
*
825498 AAAAACATAAAAGATAAA
1 AAAAACACAAAA-ATAAA
825516 AAAAACACAAAAATAAA
1 AAAAACACAAAAATAAA
825533 AA
1 AA
825535 GGCAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAAACACAAAAATAAA
Found at i:826185 original size:213 final size:214
Alignment explanation
Indices: 825949--826358 Score: 687
Period size: 213 Copynumber: 1.9 Consensus size: 214
825939 CTCATACCGG
* *
825949 TTAGGTTAATTGTTTGAGAAAGATCTCGAGATGCATAAAAAAAACATTTGTATCATGATTATCAG
1 TTAGGTTAATTATTCGAGAAAGATCTCGAGATGCATAAAAAAAACATTTGTATCATGATTATCAG
* *
826014 GGACATGAATAGCCCAAATTGCATCACCCTTGTAGCCATCAAACCATTTTGTTAGAAGTAAACCA
66 GGACATCAATAGCCCAAATTGCATCACCCTTCTAGCCATCAAACCATTTTGTTAGAAGTAAACCA
*
826079 TCACCTTTCTTGTC-AAAAAAATTGAATTGTATCACATTTCTTGTCAAGCAGGCCTTTCGTCAGA
131 TCACCTTTCTTGTCAAAAAAAATTGAATTATATCACATTTCTTGTCAAGCAGGCCTTTCGTCAGA
826143 AAAACATTACTAATACCTA
196 AAAACATTACTAATACCTA
* * * *
826162 TTAGGTTGATTATTCGAGAAAGATCTCGAGATGCATCAGAAAAACATTTGTGTCATGATTATCAG
1 TTAGGTTAATTATTCGAGAAAGATCTCGAGATGCATAAAAAAAACATTTGTATCATGATTATCAG
* *
826227 GGACATCAATAGCCCAAATTGCATCACCCTTCTAGCCATCAAATCATTTTGTTGGAAGTAAACCA
66 GGACATCAATAGCCCAAATTGCATCACCCTTCTAGCCATCAAACCATTTTGTTAGAAGTAAACCA
* * *
826292 TCACTTTTCTTGTCAAAAAAAATTGAATTATATCACATTTCTTGTCAAGCAGTCTTTTCGTCAGA
131 TCACCTTTCTTGTCAAAAAAAATTGAATTATATCACATTTCTTGTCAAGCAGGCCTTTCGTCAGA
826357 AA
196 AA
826359 TAAACCAAAT
Statistics
Matches: 182, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
213 133 0.73
214 49 0.27
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (214 bp):
TTAGGTTAATTATTCGAGAAAGATCTCGAGATGCATAAAAAAAACATTTGTATCATGATTATCAG
GGACATCAATAGCCCAAATTGCATCACCCTTCTAGCCATCAAACCATTTTGTTAGAAGTAAACCA
TCACCTTTCTTGTCAAAAAAAATTGAATTATATCACATTTCTTGTCAAGCAGGCCTTTCGTCAGA
AAAACATTACTAATACCTA
Found at i:827103 original size:30 final size:31
Alignment explanation
Indices: 827051--827170 Score: 93
Period size: 30 Copynumber: 3.8 Consensus size: 31
827041 ATGTAACCTC
* * *
827051 TTCAAAGTCCACGATTCAGTGGCA-TTTCTT
1 TTCAAAGTCCACAACTCCGTGGCACTTTCTT
827081 TTCAAAGTCCACAACTCCGTGGCAACCTTT-TT
1 TTCAAAGTCCACAACTCCGTGGC-A-CTTTCTT
* * * *
827113 CTATTAAAGTCCATAACTCCGTGACACCTTCCCTT
1 -T-TCAAAGTCCACAACTCCGTGGCA-CTT-TCTT
*
827148 TT-TAAGTCCACAACTCCGTGGCA
1 TTCAAAGTCCACAACTCCGTGGCA
827171 ACCTTTTTCT
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
30 20 0.27
31 1 0.01
32 20 0.27
33 10 0.14
34 20 0.27
35 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (31 bp):
TTCAAAGTCCACAACTCCGTGGCACTTTCTT
Found at i:827131 original size:34 final size:34
Alignment explanation
Indices: 827075--827196 Score: 149
Period size: 34 Copynumber: 3.6 Consensus size: 34
827065 TTCAGTGGCA
827075 TTTCTTTTCAAAGTCCACAACTCCGTGGCAACCTT
1 TTTCTTTT-AAAGTCCACAACTCCGTGGCAACCTT
* * *
827110 TTTCTATTAAAGTCCATAACTCCGTGAC-ACC-T
1 TTTCTTTTAAAGTCCACAACTCCGTGGCAACCTT
** *
827142 TCCCTTTTTAAGTCCACAACTCCGTGGCAACCTT
1 TTTCTTTTAAAGTCCACAACTCCGTGGCAACCTT
* *
827176 TTTCTGTTAAAGCCCACAACT
1 TTTCTTTTAAAGTCCACAACT
827197 TTATGGCACT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
32 23 0.32
33 6 0.08
34 35 0.49
35 7 0.10
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.34
Consensus pattern (34 bp):
TTTCTTTTAAAGTCCACAACTCCGTGGCAACCTT
Found at i:827159 original size:66 final size:66
Alignment explanation
Indices: 827085--827303 Score: 252
Period size: 66 Copynumber: 3.4 Consensus size: 66
827075 TTTCTTTTCA
* *
827085 AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCATAACTCCGTGACACCTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
827150 T
66 T
* * *** *
827151 AAGTCCACAACTCCGTGGCAACCTTTTTCTGTTAAAGCCCACAACTTTATGGCACTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
827216 T
66 T
* * ** *
827217 AAGTCCATAATTTTGTGGCAA-C-----CTATTAAAATCCACAACTCCGTGGCACCTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
827276 T
66 T
** *
827277 AAGTCCACAACTCTATGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCAACCTTTT
827304 AAGTCTACAA
Statistics
Matches: 124, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
60 47 0.38
61 1 0.01
65 1 0.01
66 75 0.60
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (66 bp):
AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
T
Found at i:827163 original size:32 final size:32
Alignment explanation
Indices: 827078--827352 Score: 155
Period size: 32 Copynumber: 8.9 Consensus size: 32
827068 AGTGGCATTT
**
827078 CTTTTCAAAGTCCACAACTCCGTGGCAACCTTTTT
1 CTTTT-AAAGTCCACAACTCCGTGGC-ACC-TTCC
* * *
827113 CTATTAAAGTCCATAACTCCGTGACACCTTCC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
* **
827145 CTTTTTAAGTCCACAACTCCGTGGCAACCTTTTT
1 CTTTTAAAGTCCACAACTCCGTGGC-ACC-TTCC
* * *** *
827179 CTGTTAAAGCCCACAACTTTATGGCACTTTCC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
* * * ** *
827211 CTTTTTAAGTCCATAATTTTGTGGCA----AC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
* *
827239 CTATTAAAATCCACAACTCCGTGGCACCTTCC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
* **
827271 CTTTTTAAGTCCACAACTCTATGGCA----CC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
* *
827299 CTTTT-AAGTCTACAACTCTGTGGCA----CC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
*
827326 CTTTT-AAGTCCACAACTTCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
827353 CTTTTAAGTC
Statistics
Matches: 187, Mismatches: 45, Indels: 22
0.74 0.18 0.09
Matches are distributed among these distances:
27 42 0.22
28 27 0.14
32 67 0.36
33 8 0.04
34 39 0.21
35 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (32 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCTTCC
Found at i:827275 original size:60 final size:62
Alignment explanation
Indices: 827085--827369 Score: 227
Period size: 66 Copynumber: 4.7 Consensus size: 62
827075 TTTCTTTTCA
* *
827085 AAGTCCACAACTCCGTGGCAACCTTTTTCTATTAAAGTCCATAACTCCGTGACACCTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAACC----TCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
827150 T
62 T
* * *** *
827151 AAGTCCACAACTCCGTGGCAACCTTTTTCTGTTAAAGCCCACAACTTTATGGCACTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAACC----TCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTT
827216 T
62 T
* * ** *
827217 AAGTCCATAATTTTGTGGCAA-C-CTATTAAAATCCACAACTCCGTGGCACCTTCCCTTTTT
1 AAGTCCACAACTCCGTGGCAACCTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTTT
** * * *
827277 AAGTCCACAACTCTATGGC-ACC-CT-TTTAAGTCTACAACTCTGTGGCA----CCC-TTTT
1 AAGTCCACAACTCCGTGGCAACCTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTTT
* *
827331 AAGTCCACAACTTCGTGGC-ACC-CT-TTTAAGTCCACAACT
1 AAGTCCACAACTCCGTGGCAACCTCTATTAAAGTCCACAACT
827370 ATGTGGCATC
Statistics
Matches: 187, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
54 39 0.21
55 3 0.02
59 20 0.11
60 49 0.26
65 1 0.01
66 75 0.40
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (62 bp):
AAGTCCACAACTCCGTGGCAACCTCTATTAAAGTCCACAACTCCGTGGCACCTTCCCTTTTT
Found at i:827308 original size:27 final size:27
Alignment explanation
Indices: 827213--827386 Score: 179
Period size: 27 Copynumber: 6.2 Consensus size: 27
827203 CACTTTCCCT
* * * *
827213 TTTTAAGTCCATAATTTTGTGGCAACC
1 TTTTAAGTCCACAACTCTGTGGCACCC
* * *
827240 TATTAAAATCCACAACTCCGTGGCACCTTCCC
1 T-TTTAAGTCCACAACTCTGTGGCA----CCC
*
827272 TTTTTAAGTCCACAACTCTATGGCACCC
1 -TTTTAAGTCCACAACTCTGTGGCACCC
*
827300 TTTTAAGTCTACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCTGTGGCACCC
827327 TTTTAAGTCCACAACT-TCGTGGCACCC
1 TTTTAAGTCCACAACTCT-GTGGCACCC
* *
827354 TTTTAAGTCCACAACTATGTGGCATCC
1 TTTTAAGTCCACAACTCTGTGGCACCC
827381 TTTTAA
1 TTTTAA
827387 AGCTCACAAG
Statistics
Matches: 124, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 80 0.65
28 21 0.17
32 21 0.17
33 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCTGTGGCACCC
Found at i:827403 original size:28 final size:28
Alignment explanation
Indices: 827318--827853 Score: 162
Period size: 28 Copynumber: 18.1 Consensus size: 28
827308 CTACAACTCT
* * *
827318 GTGGCACCCTTTT-AAG-TCCACAACTTC
1 GTGGCATCCTTTTAAAGCT-CACAAGTTA
* *
827345 GTGGCACCCTTTT-AAG-TCCACAA-CTA
1 GTGGCATCCTTTTAAAGCT-CACAAGTTA
827371 TGTGGCATCCTTTTAAAGCTCACAAGTTA
1 -GTGGCATCCTTTTAAAGCTCACAAGTTA
* * *
827400 GTGGCACCCTTCATTAAAGCCTACACAAATTG
1 GTGGCATCCTT--TTAAAG-CT-CACAAGTTA
* *
827432 GTGACAACCCTTTCTAAAG-TCCATACAAGTCT-
1 GTGGC-ATCCTTT-TAAAGCT-C--ACAAGT-TA
* * * *
827464 GTGGCATCCCCCTTCAAAGCCCACACAAGTTG
1 GTGGCAT--CCTTTTAAAG--CTCACAAGTTA
* * * *
827496 GTGGCATCTTTTTTTTCAAAGCCCATAAGTCA
1 GTGGCATC---CTTTT-AAAGCTCACAAGTTA
* * *
827528 ATGGCATCCTTTCAAAGCCTACACAAGTTG
1 GTGGCATCCTTTTAAAG-CT-CACAAGTTA
* *
827558 GTGGCATCTTTTTTTCAAAGC-CATAAGTTA
1 GTGGCATC--CTTTT-AAAGCTCACAAGTTA
* * * *
827588 GTGGCA-CTCTTTCAAGGCCCACAAGTCA
1 GTGGCATC-CTTTTAAAGCTCACAAGTTA
* * *
827616 GTGGCACCCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTT-AAAGCTCACAAGTTA
* * *
827645 GTGGCA-CCATTCTAAAG-TGCACATAATTCT
1 GTGGCATCC-TTTTAAAGCT-CACA-AGTT-A
* * * *
827675 GTGGCAATCCCCTTCAAAGCCCACACAAGCTA
1 GTGGC-AT-CCTTTTAAAG--CTCACAAGTTA
** *
827707 GTGGCATTTTTTTTTTCAAAGCCCACAAGTTA
1 GTGGCA---TCCTTTT-AAAGCTCACAAGTTA
* * *
827739 GTGGCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTTAAAGCTCACAAGTTA
* * *
827767 GTGGCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTTAAAGCTCACAAGTTA
*
827795 GTGGCAT-CTTTTCAAAG-TCTACAAGTCA
1 GTGGCATCCTTTT-AAAGCTC-ACAAGTTA
* *
827823 GTGGCATCCTTTTAAAGCCCACAAGTAA
1 GTGGCATCCTTTTAAAGCTCACAAGTTA
827851 GTG
1 GTG
827854 ACCTCTTCTC
Statistics
Matches: 393, Mismatches: 67, Indels: 97
0.71 0.12 0.17
Matches are distributed among these distances:
26 1 0.00
27 44 0.11
28 135 0.34
29 44 0.11
30 40 0.10
31 7 0.02
32 85 0.22
33 23 0.06
34 14 0.04
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (28 bp):
GTGGCATCCTTTTAAAGCTCACAAGTTA
Found at i:827477 original size:34 final size:32
Alignment explanation
Indices: 827415--827503 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
827405 ACCCTTCATT
* * * * *
827415 AAAGCCTACACAAATTGGTGACA-ACCCTTTC
1 AAAGCCCACACAAGTTGGTGGCATCCCCCTTC
* *
827446 TAAAGTCCATACAAGTCT-GTGGCATCCCCCTTC
1 -AAAGCCCACACAAGT-TGGTGGCATCCCCCTTC
827479 AAAGCCCACACAAGTTGGTGGCATC
1 AAAGCCCACACAAGTTGGTGGCATC
827504 TTTTTTTTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 1 0.02
32 37 0.82
33 7 0.16
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (32 bp):
AAAGCCCACACAAGTTGGTGGCATCCCCCTTC
Found at i:827600 original size:60 final size:62
Alignment explanation
Indices: 827476--827610 Score: 204
Period size: 60 Copynumber: 2.2 Consensus size: 62
827466 GGCATCCCCC
827476 TTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTCAAAGCCCATAAGTCAATGGCATCCT
1 TTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTCAAAGCCCATAAGTCAATGGCATCCT
* * *
827538 TTCAAAGCCTACACAAGTTGGTGGCATC-TTTTTTTCAAAG-CCATAAGTTAGTGGCA-CTCT
1 TTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTCAAAGCCCATAAGTCAATGGCATC-CT
*
827598 TTCAAGGCCCACA
1 TTCAAAGCCCACA
827611 AGTCAGTGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.01
60 27 0.40
61 12 0.18
62 27 0.40
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (62 bp):
TTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTCAAAGCCCATAAGTCAATGGCATCCT
Found at i:829150 original size:50 final size:50
Alignment explanation
Indices: 829090--829200 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
829080 ACAATACATA
** * *
829090 TATCGATACATTCTATTTTTT-ACTTAGATGTATCGATATATTTTTCAATG
1 TATCGATACATTCT-TTTTTTAACCCAAATGTATCGATACATTTTTCAATG
829140 TATCGATACATTCTTTTTTTAACCCAAATGTATCGATACATTTTTCAATG
1 TATCGATACATTCTTTTTTTAACCCAAATGTATCGATACATTTTTCAATG
*
829190 TATTGATACAT
1 TATCGATACAT
829201 CTAGTTAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 6 0.11
50 49 0.89
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (50 bp):
TATCGATACATTCTTTTTTTAACCCAAATGTATCGATACATTTTTCAATG
Found at i:832457 original size:16 final size:15
Alignment explanation
Indices: 832426--832473 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
832416 TCTCTCTTTA
*
832426 TTTTTGCTTCTT-TT
1 TTTTTTCTTCTTGTT
832440 TTTTTTCTTGCTTGTT
1 TTTTTTCTT-CTTGTT
*
832456 TTTCTTCTTTCTTGTT
1 TTTTTTC-TTCTTGTT
832472 TT
1 TT
832474 CTTGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
16 16 0.55
17 2 0.07
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTCTTGTT
Found at i:832473 original size:28 final size:27
Alignment explanation
Indices: 832426--832485 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
832416 TCTCTCTTTA
*
832426 TTTTTGCTTCTTTTTTTTTTCTTGCTTG
1 TTTTTGCTTCTTTTTGTTTTCTTG-TTG
*
832454 TTTTT-CTTCTTTCTTGTTTTCTTGTTT
1 TTTTTGCTTCTTT-TTGTTTTCTTGTTG
832481 TTTTT
1 TTTTT
832486 ATTGCCCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.78
Consensus pattern (27 bp):
TTTTTGCTTCTTTTTGTTTTCTTGTTG
Found at i:833160 original size:15 final size:15
Alignment explanation
Indices: 833140--833174 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
833130 GCACTTAATT
833140 TTTTTTGTTTTTTCC
1 TTTTTTGTTTTTTCC
*
833155 TTTTTTGTTTTTTTC
1 TTTTTTGTTTTTTCC
833170 TTTTT
1 TTTTT
833175 CAAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (15 bp):
TTTTTTGTTTTTTCC
Found at i:836049 original size:33 final size:32
Alignment explanation
Indices: 836007--836070 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
835997 TACAAGCCAA
* *
836007 TGTATCGATACATTTTGGGATGTATTGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
836040 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
836071 AACAACTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:836170 original size:13 final size:13
Alignment explanation
Indices: 836152--836176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
836142 ACATTTGGTC
836152 ATGTATCGATACA
1 ATGTATCGATACA
836165 ATGTATCGATAC
1 ATGTATCGATAC
836177 TGTGCAATCT
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):
ATGTATCGATACA
Found at i:836750 original size:22 final size:23
Alignment explanation
Indices: 836711--836756 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
836701 TTTTCTTTTC
836711 TCTCCCCCTTAATCAAAAAAATT
1 TCTCCCCCTTAATCAAAAAAATT
*
836734 TCTCCCCCTTAAT-AAAATAATT
1 TCTCCCCCTTAATCAAAAAAATT
836756 T
1 T
836757 AACAATTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (23 bp):
TCTCCCCCTTAATCAAAAAAATT
Found at i:838873 original size:8 final size:8
Alignment explanation
Indices: 838855--838885 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
838845 TTTTCAACAT
838855 CAAATATCA
1 CAAA-ATCA
838864 CAAAATCA
1 CAAAATCA
838872 CAAAATCA
1 CAAAATCA
838880 CAAAAT
1 CAAAAT
838886 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (8 bp):
CAAAATCA
Found at i:839782 original size:39 final size:39
Alignment explanation
Indices: 839723--839804 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
839713 AATTACCTCC
839723 TTCAACTTTTTCTAGCTTTGTTGTTGTACTCATTGGAGT
1 TTCAACTTTTTCTAGCTTTGTTGTTGTACTCATTGGAGT
*
839762 TTCATCTTTTTCTAGCTTTGTTGTTGTACTCATTGGAGT
1 TTCAACTTTTTCTAGCTTTGTTGTTGTACTCATTGGAGT
839801 TTCA
1 TTCA
839805 CATGGCTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.15, C:0.16, G:0.17, T:0.52
Consensus pattern (39 bp):
TTCAACTTTTTCTAGCTTTGTTGTTGTACTCATTGGAGT
Found at i:843237 original size:19 final size:19
Alignment explanation
Indices: 843213--843310 Score: 112
Period size: 19 Copynumber: 5.8 Consensus size: 19
843203 TGTCAACGAT
843213 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
843232 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
843246 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
843264 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
843278 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
843296 TTGTATCGATACATA
1 TTGTATCGATACATA
843311 TGAAGCTACT
Statistics
Matches: 67, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 37 0.55
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:843250 original size:32 final size:32
Alignment explanation
Indices: 843214--843308 Score: 190
Period size: 32 Copynumber: 3.0 Consensus size: 32
843204 GTCAACGATT
843214 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
843246 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
843278 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
843309 TATGAAGCTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:843251 original size:13 final size:13
Alignment explanation
Indices: 843233--843289 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
843223 ACATAAGTGT
843233 TGTATCGATACAA
1 TGTATCGATACAA
843246 TGTATCGATACATAA
1 TGTATCGATAC--AA
843261 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
843278 TGTATCGATACA
1 TGTATCGATACA
843290 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:857282 original size:16 final size:16
Alignment explanation
Indices: 857259--857352 Score: 81
Period size: 16 Copynumber: 5.8 Consensus size: 16
857249 GCGTCCTCCG
857259 CAAAAAAAAACAAAAA
1 CAAAAAAAAACAAAAA
857275 CAACAAAAATAAACAAAAA
1 C-A-AAAAA-AAACAAAAA
*
857294 -AACAAAAAGA-AAAAA
1 CAA-AAAAAAACAAAAA
*
857309 -GAAAAAAAAC-AAAA
1 CAAAAAAAAACAAAAA
857323 CAAAATAAAAAC-AAAA
1 CAAAA-AAAAACAAAAA
857339 CAGAAAAAAAACAA
1 CA-AAAAAAAACAA
857353 CAAAAAGGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
14 10 0.15
15 9 0.14
16 22 0.34
17 10 0.15
18 5 0.08
19 9 0.14
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (16 bp):
CAAAAAAAAACAAAAA
Found at i:857292 original size:27 final size:26
Alignment explanation
Indices: 857260--857358 Score: 87
Period size: 27 Copynumber: 3.6 Consensus size: 26
857250 CGTCCTCCGC
*
857260 AAAAAAAAACAAAAACAACAAAA-ATA
1 AAAAAAAAACAAAAAAAACAAAACA-A
857286 AACAAAAAAACAAAAAGAAA-AAAGA-AA
1 AA-AAAAAAACAAAAA-AAACAAA-ACAA
857313 AAAAACAAAACAAAATAAAAACAAAACAGA
1 AAAAA-AAAAC-AAA-AAAAACAAAACA-A
857343 AAAAAAACAACAAAAA
1 AAAAAAA-AACAAAAA
857359 GGGTCCGGAT
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
26 5 0.08
27 24 0.39
28 13 0.21
29 11 0.18
30 9 0.15
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (26 bp):
AAAAAAAAACAAAAAAAACAAAACAA
Found at i:857296 original size:21 final size:20
Alignment explanation
Indices: 857270--857358 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 20
857260 AAAAAAAAAC
857270 AAAAACAACAAAAATAAACAA
1 AAAAACAA-AAAAATAAACAA
* *
857291 AAAAACAAAAAGAAAAAAGAAA
1 AAAAACAAAAA-AATAAA-CAA
857313 AAAAACAAAACAAAATAAA-AA
1 AAAAAC-AAA-AAAATAAACAA
* *
857334 CAAAACAGAAAAA-AAACAA
1 AAAAACAAAAAAATAAACAA
857353 CAAAAA
1 -AAAAA
857359 GGGTCCGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.05
19 6 0.11
20 9 0.16
21 20 0.36
22 8 0.14
23 8 0.14
24 2 0.04
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.02
Consensus pattern (20 bp):
AAAAACAAAAAAATAAACAA
Found at i:857333 original size:32 final size:31
Alignment explanation
Indices: 857261--857358 Score: 105
Period size: 32 Copynumber: 3.3 Consensus size: 31
857251 GTCCTCCGCA
* *
857261 AAAAAAAACAAAAAC--AACA-AAAATAAAC
1 AAAAAAAACAAAAACAAAAAAGAAAAAAAAC
*
857289 -AAAAAAACAAAAAGAAAAAAGAAAAAAAAC
1 AAAAAAAACAAAAACAAAAAAGAAAAAAAAC
* *
857319 AAAACAAAATAAAAACAAAACAGAAAAAAAAC
1 AAAA-AAAACAAAAACAAAAAAGAAAAAAAAC
*
857351 AACAAAAA
1 AAAAAAAA
857359 GGGTCCGGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
27 13 0.22
29 3 0.05
30 8 0.14
31 7 0.12
32 27 0.47
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (31 bp):
AAAAAAAACAAAAACAAAAAAGAAAAAAAAC
Found at i:857358 original size:1 final size:1
Alignment explanation
Indices: 857260--857349 Score: 54
Period size: 1 Copynumber: 90.0 Consensus size: 1
857250 CGTCCTCCGC
* * * * * * * * * *
857260 AAAAAAAAACAAAAACAACAAAAATAAACAAAAAAACAAAAAGAAAAAAGAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
857325 AAATAAAAACAAAACAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
857350 CAACAAAAAG
Statistics
Matches: 61, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.84, C:0.10, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:858842 original size:29 final size:29
Alignment explanation
Indices: 858803--859093 Score: 169
Period size: 29 Copynumber: 9.7 Consensus size: 29
858793 TCACCCTTCA
*
858803 AAAGCCCACAAATCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
858832 AAAGCCCACAAGTCAGTGACATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
858861 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
** * * *
858888 AAAGCCCACAAACCACT-GCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
858916 TGAAGCCCACAAGTTAATGGCATCTTTTCC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
858946 AAAGTCCACAACTCCGTGGCACTCCTTTTCTTTTG
1 AAAGCCCACAAGTCAGTGGCA-T-C---T-TTTTC
* * * *
858981 TAAGCCCACAACTCCGTAGCACTCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
859012 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
859044 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
859072 AAAAGCCCACAAGTCAGTGGCA
1 -AAAGCCCACAAGTCAGTGGCA
859094 ACCTTCAAAA
Statistics
Matches: 205, Mismatches: 43, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
26 4 0.02
27 16 0.08
28 28 0.14
29 74 0.36
30 33 0.16
31 2 0.01
32 1 0.00
33 5 0.02
34 19 0.09
35 23 0.11
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:858895 original size:85 final size:87
Alignment explanation
Indices: 858797--859093 Score: 258
Period size: 85 Copynumber: 3.3 Consensus size: 87
858787 CATTCCTCAC
* * *
858797 CCTTCAAAAGCCCACAAATCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGACATCTTTTTC
1 CCTTCTAAAGCCCACAAATCAGTGGCATCTTTTTCTAAAGCCCACAAGTTAGTGGCATCTTTTTC
858861 AAAGTCCACAAGTCAGTGGCAA
66 AAAGTCCACAAGTCAGTGGCAA
* * * * * * *
858883 CCTTC-AAAGCCCACAAACCACT-GCACCCTTTTCTGAAGCCCACAAGTTAATGGCATCTTTTCC
1 CCTTCTAAAGCCCACAAATCAGTGGCATCTTTTTCTAAAGCCCACAAGTTAGTGGCATCTTTTTC
* * *
858946 AAAGTCCACAACTCCGTGGCACT
66 AAAGTCCACAAGTCAGTGGCA-A
* * * * *
858969 CCTTTTCTTTTGTAAGCCCACAACTCCGTAGCACTCTTTTTCCTTTTAAGCCCACAAGTTAGTGG
1 CC--TTC---T-AAAGCCCACAAATCAGTGGCA-TCTTTTT-C--TAAAGCCCACAAGTTAGTGG
* * *
859034 CACCCTTTTCAAAAGCCCACAAGTCAGTGGCAA
56 CATCTTTTTC-AAAGTCCACAAGTCAGTGGCAA
* *
859067 CCTTCAAAAGCCCACAAGTCAGTGGCA
1 CCTTCTAAAGCCCACAAATCAGTGGCA
859094 ACCTTCAAAA
Statistics
Matches: 163, Mismatches: 33, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
84 9 0.06
85 58 0.36
86 7 0.04
88 3 0.02
92 17 0.10
93 12 0.07
94 3 0.02
95 5 0.03
96 4 0.02
98 27 0.17
99 18 0.11
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (87 bp):
CCTTCTAAAGCCCACAAATCAGTGGCATCTTTTTCTAAAGCCCACAAGTTAGTGGCATCTTTTTC
AAAGTCCACAAGTCAGTGGCAA
Found at i:858926 original size:56 final size:57
Alignment explanation
Indices: 858803--858956 Score: 132
Period size: 56 Copynumber: 2.7 Consensus size: 57
858793 TCACCCTTCA
* * * ** * * *
858803 AAAGCCCACAAATCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGACATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAACCACTGACACCCTTTTC
*
858861 AAAGTCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAACCACTG-CACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAACCACTGACACCCTTTTC
* * * * * *
858916 TGAAGCCCACAAGTTAATGGCATCTTTTCCAAAGTCCACAA
1 -AAAGCCCACAAGTCAGTGGCAACTCTT-CAAAGCCCACAA
858957 CTCCGTGGCA
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
55 8 0.10
56 36 0.47
57 2 0.03
58 31 0.40
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAACCACTGACACCCTTTTC
Found at i:858991 original size:35 final size:34
Alignment explanation
Indices: 858951--859043 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
858941 TTTCCAAAGT
*
858951 CCACAACTCCGTGGCACTCCTTTTCTTTTGTAAGC
1 CCACAACTCCGTGGCACTCCTTTTCCTTT-TAAGC
* *
858986 CCACAACTCCGTAGCACTCTTTTTCCTTTTAAGC
1 CCACAACTCCGTGGCACTCCTTTTCCTTTTAAGC
* **
859020 CCACAAGTTAGTGGCAC-CCTTTTC
1 CCACAACTCCGTGGCACTCCTTTTC
859044 AAAAGCCCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
33 6 0.12
34 18 0.36
35 26 0.52
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.33
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCCTTTTCCTTTTAAGC
Found at i:859042 original size:34 final size:35
Alignment explanation
Indices: 858951--859042 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 35
858941 TTTCCAAAGT
* *
858951 CCACAACTCCGTGGCACTCC-TTTTCTTTTGTAAGC
1 CCACAACTCAGTGGCAC-CCTTTTTCCTTTGTAAGC
* * *
858986 CCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCAGTGGCACCCTTTTTCCTTTGTAAGC
* *
859020 CCACAAGTTAGTGGCACCCTTTT
1 CCACAACTCAGTGGCACCCTTTT
859043 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 24 0.50
35 24 0.50
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.34
Consensus pattern (35 bp):
CCACAACTCAGTGGCACCCTTTTTCCTTTGTAAGC
Found at i:859081 original size:28 final size:28
Alignment explanation
Indices: 859016--859113 Score: 151
Period size: 28 Copynumber: 3.4 Consensus size: 28
859006 TTTTCCTTTT
* *
859016 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTCAA
859046 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
859074 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
859102 AAGCACACAAGT
1 AAGCCCACAAGT
859114 TGATGCAACC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
28 44 0.68
30 21 0.32
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.16
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAA
Found at i:869329 original size:13 final size:13
Alignment explanation
Indices: 869288--869335 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
869278 GGAAAACCTA
869288 AATGTATCGATAC
1 AATGTATCGATAC
869301 AATG-ATC--T--
1 AATGTATCGATAC
869309 AA-GTATCGATAC
1 AATGTATCGATAC
869321 AATGTATCGATAC
1 AATGTATCGATAC
869334 AA
1 AA
869336 GGTTACTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 5 0.17
10 2 0.07
12 5 0.17
13 16 0.55
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:871989 original size:20 final size:19
Alignment explanation
Indices: 871946--871998 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
871936 ACGTTATGCT
* *
871946 TTGTATCGATACATGCTCA
1 TTGTATCGATATATACTCA
871965 TTGTATCGATATATACTCAA
1 TTGTATCGATATATACTC-A
871985 TTGTATCGATATAT
1 TTGTATCGATATAT
871999 GAATCTAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (19 bp):
TTGTATCGATATATACTCA
Found at i:872505 original size:23 final size:23
Alignment explanation
Indices: 872478--872521 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
872468 GCATTCAACC
*
872478 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
872501 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
872522 GATTGTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:876170 original size:11 final size:11
Alignment explanation
Indices: 876154--876183 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
876144 AATTAAATCA
876154 ACAAGAAAATT
1 ACAAGAAAATT
876165 ACAAGAAAATT
1 ACAAGAAAATT
876176 ACAAGAAA
1 ACAAGAAA
876184 CGTGGCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (11 bp):
ACAAGAAAATT
Found at i:877547 original size:22 final size:22
Alignment explanation
Indices: 877513--877555 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
877503 AGTTTAGTAT
877513 AAATGTTTTTCAAGTAATAAATC
1 AAATGTTTTTCAAGTAA-AAATC
877536 AAATG-TTTTCAAGTAAAAAT
1 AAATGTTTTTCAAGTAAAAAT
877556 AATCCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATGTTTTTCAAGTAAAAATC
Found at i:877692 original size:13 final size:13
Alignment explanation
Indices: 877674--877698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
877664 ATATTGCTTA
877674 GTATCGATACATT
1 GTATCGATACATT
877687 GTATCGATACAT
1 GTATCGATACAT
877699 GTTCTTGGTA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:877715 original size:32 final size:33
Alignment explanation
Indices: 877653--877716 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
877643 ACACACCAGA
877653 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* *
877686 TGTATCGATACATGTT-CTTGGTATCGATACA
1 TGTATCGATACATATTGCTTAGTATCGATACA
877717 AAATGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:878074 original size:72 final size:72
Alignment explanation
Indices: 877957--878113 Score: 296
Period size: 72 Copynumber: 2.2 Consensus size: 72
877947 ACTAAGCAAA
877957 ATGTATCGATACATCTGGGTTTGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCA
1 ATGTATCGATACATCTGGGTTTGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCA
878022 ACGTTTT
66 ACGTTTT
*
878029 ATGTATCGATACATCTGGGTTTGTATTGATACAATCAAGGGTTTTGACCTTTCTAGCTTAAGTCA
1 ATGTATCGATACATCTGGGTTTGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCA
*
878094 ACTTTTT
66 ACGTTTT
878101 ATGTATCGATACA
1 ATGTATCGATACA
878114 AATACCTATG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 83 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (72 bp):
ATGTATCGATACATCTGGGTTTGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCA
ACGTTTT
Found at i:878126 original size:72 final size:72
Alignment explanation
Indices: 877978--878132 Score: 229
Period size: 72 Copynumber: 2.2 Consensus size: 72
877968 CATCTGGGTT
*
877978 TGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCAACGTTTTATGTATCGATACAT
1 TGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCAACGTTTTATGTATCGATACAA
* *** *
878043 CTGGGTT
66 ATACCTA
* *
878050 TGTATTGATACAATCAAGGGTTTTGACCTTTCTAGCTTAAGTCAACTTTTTATGTATCGATACAA
1 TGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCAACGTTTTATGTATCGATACAA
878115 ATACCTA
66 ATACCTA
*
878122 TGTATCGATAC
1 TGTATTGATAC
878133 TTTGAGTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (72 bp):
TGTATTGATACAATCAAGGATTTTGACCTTTCTAGCTTAAGTCAACGTTTTATGTATCGATACAA
ATACCTA
Found at i:880615 original size:15 final size:15
Alignment explanation
Indices: 880585--880620 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
880575 TATACATATT
880585 AATTTTTCTCCATAA
1 AATTTTTCTCCATAA
880600 AGATTTTTCTCC-TAA
1 A-ATTTTTCTCCATAA
880615 AATTTT
1 AATTTT
880621 ATGAGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 5 0.25
16 10 0.50
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTTTTCTCCATAA
Found at i:880720 original size:5 final size:5
Alignment explanation
Indices: 880688--880741 Score: 63
Period size: 5 Copynumber: 10.0 Consensus size: 5
880678 ATAATTATTA
*
880688 ATTTT AATTTT CTTTT AATTTT GGATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT -ATTTT ATTTT -ATTTT --ATTTT ATTTT ATTTT ATTTT ATTTT
880737 ATTTT
1 ATTTT
880742 CTACTAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
5 29 0.67
6 9 0.21
7 5 0.12
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:880936 original size:13 final size:14
Alignment explanation
Indices: 880913--880941 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
880903 TAAATATCAT
880913 AAAATAAAATAAAG
1 AAAATAAAATAAAG
880927 AAAA-AAAATAAAG
1 AAAATAAAATAAAG
880940 AA
1 AA
880942 CCATTTGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAATAAAATAAAG
Found at i:884639 original size:91 final size:89
Alignment explanation
Indices: 884544--884715 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 89
884534 CCCCATTATT
* * * *
884544 TCGAAGGGATACTCCAA-ACCTACTCTTCAAAAAAAAAATC-AAATTTTCCTTCGAGGAATTTTA
1 TCGAAGGGAAAATCCAACACCT-CTCTTC--AAAAAAAATCAAAATTTT-CTTCAAAGAATTTTA
* *
884607 TCTTTAGAGAAACTCCATCCTCACTCAC
62 TCCTCAGAGAAACTCCATCCTCACTCAC
* * *
884635 TCGAAGGGAAAATCCAACCCCTCTCTTCAAAAAAAATCAAAATTTTTTTCAAATAATTTTATCCT
1 TCGAAGGGAAAATCCAACACCTCTCTTCAAAAAAAATCAAAATTTTCTTCAAAGAATTTTATCCT
884700 CAGAGAAACTCCATCC
66 CAGAGAAACTCCATCC
884716 CTATTATTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
89 39 0.56
90 7 0.10
91 21 0.30
92 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (89 bp):
TCGAAGGGAAAATCCAACACCTCTCTTCAAAAAAAATCAAAATTTTCTTCAAAGAATTTTATCCT
CAGAGAAACTCCATCCTCACTCAC
Found at i:888497 original size:80 final size:79
Alignment explanation
Indices: 888162--888497 Score: 282
Period size: 80 Copynumber: 4.2 Consensus size: 79
888152 AAAACATCAA
* * * * * * * *
888162 AAGGGGTACTCCAACCCTAATTTTCACTTCTAAAACACCAAAATTTTGATATCTA-GGATACTTC
1 AAGGGATACTCCAACCC-CATTTTTACTTCTAAAACACCAAATTTTTCATCTTTAGGGATACTCC
*
888226 AACCCCACAATCTCTG
65 AACCCCACAATCTC-C
* * * * * * * * *
888242 AAGGGACATTCTAACCCCATTTTTACTTCGAAAGCATCGAATTTTTCATCTTTGGGGATACTTCA
1 AAGGGATACTCCAACCCCATTTTTACTTCTAAAACACCAAATTTTTCATCTTTAGGGATACTCCA
*
888307 ACCCCACTATCTCC
66 ACCCCACAATCTCC
* * * * * *
888321 AAAGTGAGACTCGAACCCCATTTTTACTTCCAAAACATCGAATTTTTCATCTTT-GGAGATACTC
1 -AAGGGATACTCCAACCCCATTTTTACTTCTAAAACACCAAATTTTTCATCTTTAGG-GATACTC
* * * *
888385 TAACCCTACCATTTCC
64 CAACCCCACAATCTCC
* * *
888401 AAGGGGATACTTCAACCCCATTTTTACTTCTAAAATACCAAATTCTTCATCTTTAGGGATACTCC
1 AA-GGGATACTCCAACCCCATTTTTACTTCTAAAACACCAAATTTTTCATCTTTAGGGATACTCC
*
888466 AACCCCA-ACATCTCT
65 AACCCCACA-ATCTCC
*
888481 GAGGCGATACTCCAACC
1 AAGG-GATACTCCAACC
888498 TTGATCTTCA
Statistics
Matches: 205, Mismatches: 44, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
79 32 0.16
80 171 0.83
81 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (79 bp):
AAGGGATACTCCAACCCCATTTTTACTTCTAAAACACCAAATTTTTCATCTTTAGGGATACTCCA
ACCCCACAATCTCC
Found at i:888556 original size:74 final size:74
Alignment explanation
Indices: 888472--888619 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
888462 CTCCAACCCC
888472 AACATCTCTGAGGCGATACTCCAACCTTGATCTTCACCTAAAACTTAAATTTTTACCTTTTTTAA
1 AACATCTCTGAGGCGATACTCCAACCTTGATCTTCACCTAAAACTTAAATTTTTACCTTTTTTAA
888537 ACTTTTCAA
66 ACTTTTCAA
888546 AACATCTCTGAGGCGATACTCCAACCTTGATCTTCACCTAAAACTTAAATTTTTACCTTTTTTAA
1 AACATCTCTGAGGCGATACTCCAACCTTGATCTTCACCTAAAACTTAAATTTTTACCTTTTTTAA
888611 ACTTTTCAA
66 ACTTTTCAA
888620 GCTCTTCCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (74 bp):
AACATCTCTGAGGCGATACTCCAACCTTGATCTTCACCTAAAACTTAAATTTTTACCTTTTTTAA
ACTTTTCAA
Found at i:890992 original size:20 final size:19
Alignment explanation
Indices: 890942--890995 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
890932 ACATTATGCT
**
890942 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
890961 TTATATCGATACATGGACAA
1 TTGTATCGATACATGGAC-A
*
890981 TTGTATCTATACATG
1 TTGTATCGATACATG
890996 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:891063 original size:13 final size:13
Alignment explanation
Indices: 891041--891092 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
891031 GATACTTGGC
*
891041 ACATTATATCGAT
1 ACATTGTATCGAT
891054 ACATTGTATCGAT
1 ACATTGTATCGAT
891067 ACA-TG-AT-G--
1 ACATTGTATCGAT
891075 A-ATTGTATCGAT
1 ACATTGTATCGAT
891087 ACATTG
1 ACATTG
891093 CTTCAAACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 19 0.59
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:897008 original size:13 final size:13
Alignment explanation
Indices: 896990--897015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
896980 TACACCAAGT
896990 ATGTATCGATACA
1 ATGTATCGATACA
897003 ATGTATCGATACA
1 ATGTATCGATACA
897016 CAAAAAATTG
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:897013 original size:32 final size:33
Alignment explanation
Indices: 896972--897035 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
896962 TAGCCAAACT
* **
896972 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
897004 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
897036 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:901103 original size:15 final size:15
Alignment explanation
Indices: 901083--901113 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
901073 TAAAAATGTC
*
901083 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
901098 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
901113 C
1 C
901114 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:903193 original size:13 final size:13
Alignment explanation
Indices: 903175--903213 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
903165 ACATTTTTCT
903175 TTGTATCGATACA
1 TTGTATCGATACA
903188 TTGTATCGATACA
1 TTGTATCGATACA
*
903201 CTGTATCGATACA
1 TTGTATCGATACA
903214 GGGGGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:903677 original size:20 final size:21
Alignment explanation
Indices: 903654--903696 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
903644 GGCAGCACCA
*
903654 CCAGGTCGCGACC-GGCACTC
1 CCAGGTCGCAACCAGGCACTC
*
903674 CCAGGTCGCAACCAGGCAGTC
1 CCAGGTCGCAACCAGGCACTC
903695 CC
1 CC
903697 CACACTAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.19, C:0.44, G:0.28, T:0.09
Consensus pattern (21 bp):
CCAGGTCGCAACCAGGCACTC
Found at i:905775 original size:13 final size:13
Alignment explanation
Indices: 905757--905782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
905747 TACACCAAGT
905757 ATGTATCGATACA
1 ATGTATCGATACA
905770 ATGTATCGATACA
1 ATGTATCGATACA
905783 CAAAAAATTG
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:905780 original size:32 final size:33
Alignment explanation
Indices: 905739--905802 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
905729 TAGCCAAACT
* **
905739 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
905771 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
905803 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:908060 original size:24 final size:26
Alignment explanation
Indices: 908033--908086 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
908023 TCAAAATTTT
908033 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
908057 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
908084 ATT
1 ATT
908087 TTCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
27 20 0.77
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:910750 original size:20 final size:20
Alignment explanation
Indices: 910714--910751 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
910704 TTTTTAAAAA
*
910714 TTTTATTTATTTTCTTGAGT
1 TTTTATTTATTTCCTTGAGT
910734 TTTTCATTT-TTTCCTTGA
1 TTTT-ATTTATTTCCTTGA
910752 AATCCCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.13, C:0.11, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTCCTTGAGT
Done.