Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 2 of 433
Found at i:418982 original size:21 final size:21
Alignment explanation
Indices: 418956--418996 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
418946 ATCTGCTCAA
* *
418956 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
418977 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
418997 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:421176 original size:53 final size:53
Alignment explanation
Indices: 421095--421245 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
421085 CTTACACGGT
* *
421095 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
421150 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
421203 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
421246 CACACTTGTC
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:425953 original size:35 final size:35
Alignment explanation
Indices: 425909--426075 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
425899 TCCTCATTGA
** *
425909 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
425944 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
425984 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
426019 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
426054 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
426076 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:425992 original size:75 final size:73
Alignment explanation
Indices: 425904--426075 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
425894 GGTTTTCCTC
** * * **
425904 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
425968 TCAGTATGG
65 TCAGTATGG
*
425977 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
426042 CTCAGTATGG
64 CTCAGTATGG
426052 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
426076 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:433442 original size:35 final size:35
Alignment explanation
Indices: 433398--433564 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
433388 TCCTCATTGA
** *
433398 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
433433 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
433473 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
433508 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
433543 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
433565 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:433481 original size:75 final size:73
Alignment explanation
Indices: 433393--433564 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
433383 GGTTTTCCTC
** * * **
433393 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
433457 TCAGTATGG
65 TCAGTATGG
*
433466 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
433531 CTCAGTATGG
64 CTCAGTATGG
433541 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
433565 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:436826 original size:25 final size:25
Alignment explanation
Indices: 436798--436849 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
436788 ATGTGCAACG
436798 TTATATATGAATTTTTTT-TGCAATT
1 TTATATATG-ATTTTTTTATGCAATT
*
436823 TTATATATGATTTTTTTATTCAATT
1 TTATATATGATTTTTTTATGCAATT
436848 TT
1 TT
436850 CACAAATCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (25 bp):
TTATATATGATTTTTTTATGCAATT
Found at i:440368 original size:21 final size:21
Alignment explanation
Indices: 440328--440368 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
440318 AGTGGCGGTA
* *
440328 ATATGACATTTTAGGTTGGTG
1 ATATGACATTTTAAGATGGTG
*
440349 ATATGATATTTTAAGATGGT
1 ATATGACATTTTAAGATGGT
440369 TAGATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (21 bp):
ATATGACATTTTAAGATGGTG
Found at i:442560 original size:2 final size:2
Alignment explanation
Indices: 442553--442581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
442543 TACTACATGC
442553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
442582 AAGACATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:449846 original size:22 final size:22
Alignment explanation
Indices: 449818--449861 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
449808 CATATGTCGA
449818 TTATGTATTAGTTAATTTTTTT
1 TTATGTATTAGTTAATTTTTTT
449840 TTATGTATTAGTTAATTTTTTT
1 TTATGTATTAGTTAATTTTTTT
449862 ACTCCTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (22 bp):
TTATGTATTAGTTAATTTTTTT
Found at i:451362 original size:15 final size:16
Alignment explanation
Indices: 451329--451364 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
451319 CATTTACTTT
*
451329 ATAATATTTTATAAAA
1 ATAATATTTCATAAAA
451345 ATAATATTTCAT-AAA
1 ATAATATTTCATAAAA
451360 ATAAT
1 ATAAT
451365 TGAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATTTCATAAAA
Found at i:460671 original size:31 final size:31
Alignment explanation
Indices: 460629--460704 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
460619 TAAAAAAATT
* *
460629 AATAGTCTAGTGATTTAAATAAAAATTTTGG
1 AATAGTTTAGTGACTTAAATAAAAATTTTGG
*
460660 AATAGTTTAGTGACTTAAATAAAAATTTTTG
1 AATAGTTTAGTGACTTAAATAAAAATTTTGG
* *
460691 AATAATTTAATGAC
1 AATAGTTTAGTGAC
460705 CATTTTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (31 bp):
AATAGTTTAGTGACTTAAATAAAAATTTTGG
Found at i:463506 original size:3 final size:3
Alignment explanation
Indices: 463498--463522 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
463488 TTAAATCTAG
463498 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
463523 TGGATCGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:467865 original size:2 final size:2
Alignment explanation
Indices: 467858--467888 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
467848 TTAGCTGAGC
*
467858 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
467889 GGCATATAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:469980 original size:15 final size:15
Alignment explanation
Indices: 469946--469980 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
469936 GAATATGTAA
*
469946 AAAAAAAATAATTTT
1 AAAAAAAATAAATTT
469961 AAAAAAAATAAATTT
1 AAAAAAAATAAATTT
469976 CAAAA
1 -AAAA
469981 TTATACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAAAATAAATTT
Found at i:473872 original size:17 final size:17
Alignment explanation
Indices: 473852--473885 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
473842 AATACAAACT
473852 TCATATAAATCTTATAA
1 TCATATAAATCTTATAA
473869 TCATATAAATCTTATAA
1 TCATATAAATCTTATAA
473886 GAGAATCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATATAAATCTTATAA
Found at i:474113 original size:2 final size:2
Alignment explanation
Indices: 474106--474144 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
474096 AGATACAATT
474106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
474145 GAACAATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:475872 original size:108 final size:108
Alignment explanation
Indices: 475680--475892 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
475670 GAACCTTGAT
* * * *
475680 CATTGAAGTGTTAACAAGATTAACCACTATTCTCTTATGTTGTTGACAATTTCGATTATTGATCA
1 CATTGAAATGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCA
*
475745 TGCATTCACTCTTGAATTGGATTTTCCAATGGCTTCAAATAGA
66 TGCATTCACTCTTGAATTGGATTTTCCAATCGCTTCAAATAGA
*
475788 CATTGAAATGTTAACAAGATTAACCACTACTCTTTTACGTTGTTGACAATTTCAATTATTGATCA
1 CATTGAAATGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCA
* * **
475853 TTCATTCATTCTT-AGATTGGATTTTTGAATCGCTTCAAAT
66 TGCATTCACTCTTGA-ATTGGATTTTCCAATCGCTTCAAAT
475893 GAAGGATATC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 93 0.99
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (108 bp):
CATTGAAATGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCA
TGCATTCACTCTTGAATTGGATTTTCCAATCGCTTCAAATAGA
Found at i:481408 original size:6 final size:6
Alignment explanation
Indices: 481390--481447 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
481380 AAACGCATAT
* * * *
481390 AATTAA AAATAA AATTAA AATTAA TATGTAT AGTT-A AATTAA AATTAA
1 AATTAA AATTAA AATTAA AATTAA AAT-TAA AATTAA AATTAA AATTAA
481438 AATTAA AATT
1 AATTAA AATT
481448 TTATTTTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 3 0.07
6 36 0.86
7 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:493482 original size:19 final size:19
Alignment explanation
Indices: 493437--493482 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
493427 TATGATAAAC
*
493437 TGATTTGAGGAATGTACAT
1 TGATTTGCGGAATGTACAT
493456 TGATTTGCGGAATGTACAT
1 TGATTTGCGGAATGTACAT
493475 TGATTTGC
1 TGATTTGC
493483 TACTGTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (19 bp):
TGATTTGCGGAATGTACAT
Found at i:498972 original size:22 final size:21
Alignment explanation
Indices: 498941--498994 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
498931 TAGAATATAC
* * *
498941 CCCATTCCTTGCCCATACTTTG
1 CCCATACCTTGCCCATAC-CTA
*
498963 CCCATACCTTTCCCATACCTA
1 CCCATACCTTGCCCATACCTA
498984 CCCATACCTTG
1 CCCATACCTTG
498995 GAAAGGTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (21 bp):
CCCATACCTTGCCCATACCTA
Found at i:498981 original size:11 final size:11
Alignment explanation
Indices: 498941--498993 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
498931 TAGAATATAC
* *
498941 CCCATTCCTTG
1 CCCATACCTTT
498952 CCCATA-CTTT
1 CCCATACCTTT
498962 GCCCATACCTTT
1 -CCCATACCTTT
*
498974 CCCATACC-TA
1 CCCATACCTTT
498984 CCCATACCTT
1 CCCATACCTT
498994 GGAAAGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 12 0.33
11 20 0.56
12 4 0.11
ACGTcount: A:0.19, C:0.45, G:0.04, T:0.32
Consensus pattern (11 bp):
CCCATACCTTT
Found at i:499552 original size:18 final size:18
Alignment explanation
Indices: 499529--499603 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
499519 GACCGTTTAT
499529 AGTACTATTCACGTATAC
1 AGTACTATTCACGTATAC
499547 AGTACTATTCACGTATAC
1 AGTACTATTCACGTATAC
* * *
499565 GGTACTATTTACATATAC
1 AGTACTATTCACGTATAC
* *
499583 GGTACTGTT-ACGTATAC
1 AGTACTATTCACGTATAC
499600 AGTA
1 AGTA
499604 GTTGGGATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 10 0.20
18 41 0.80
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (18 bp):
AGTACTATTCACGTATAC
Found at i:503622 original size:11 final size:11
Alignment explanation
Indices: 503602--503654 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
503592 TAGAATATAC
*
503602 CCCATTCCTTG
1 CCCATACCTTG
503613 CCCATACCTTG
1 CCCATACCTTG
*
503624 CCCATACCTTT
1 CCCATACCTTG
*
503635 CCCATACC-TA
1 CCCATACCTTG
503645 CCCATACCTT
1 CCCATACCTT
503655 AGAATGGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.19, C:0.47, G:0.04, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:507947 original size:29 final size:28
Alignment explanation
Indices: 507864--507947 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 28
507854 CTTTTATATA
*
507864 AAAAAATTTAATAATTTAGTAACTTAAAT
1 AAAAATTTTAATAATTTA-TAACTTAAAT
* ** *
507893 AAAAATTTTTAAATAGTCAATGACTTAAAT
1 AAAAA-TTTT-AATAATTTATAACTTAAAT
507923 AAAAATTTTAATAATTTTATAACTT
1 AAAAATTTTAATAA-TTTATAACTT
507948 TTTTTAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 4 0.09
29 16 0.37
30 17 0.40
31 6 0.14
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (28 bp):
AAAAATTTTAATAATTTATAACTTAAAT
Found at i:511028 original size:48 final size:48
Alignment explanation
Indices: 510934--511028 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
510924 GTAATTACCC
* * **
510934 GGGATTTCTTTCGGTTTTTCCTCTTTAAAATGAAAAGGGGGGCAACCT
1 GGGATATCTTTCGGTTTTTACTCTTTAAAATGAAAAGGGCAGCAACCT
** * *
510982 GGGATATCTTTCGGTTTTTACTCTTTTCAATGAAAATGGCATCAACC
1 GGGATATCTTTCGGTTTTTACTCTTTAAAATGAAAAGGGCAGCAACC
511029 GTCCTACAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (48 bp):
GGGATATCTTTCGGTTTTTACTCTTTAAAATGAAAAGGGCAGCAACCT
Found at i:518291 original size:6 final size:6
Alignment explanation
Indices: 518280--518342 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
518270 CAACACAGAA
518280 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
518328 ATACAT ATACAT ATA
1 ATACAT ATACAT ATA
518343 TGAGTCAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:527483 original size:20 final size:20
Alignment explanation
Indices: 527458--527497 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
527448 ATTCAATAAG
527458 AATGTGTAATCTGTAACGTT
1 AATGTGTAATCTGTAACGTT
*
527478 AATGTGTAATCTGTCACGTT
1 AATGTGTAATCTGTAACGTT
527498 CTTATTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (20 bp):
AATGTGTAATCTGTAACGTT
Found at i:528893 original size:16 final size:16
Alignment explanation
Indices: 528874--528905 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
528864 AAATGGTACA
528874 AACCCAAAATGACATG
1 AACCCAAAATGACATG
*
528890 AACCCGAAATGACATG
1 AACCCAAAATGACATG
528906 TGCAAGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
AACCCAAAATGACATG
Found at i:534534 original size:20 final size:20
Alignment explanation
Indices: 534487--534524 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
534477 CATTAAGCCC
534487 AAAAAAAACCTAACCCCCAA
1 AAAAAAAACCTAACCCCCAA
534507 AAAAAAAACCTAACCCCC
1 AAAAAAAACCTAACCCCC
534525 CCCAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.37, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAAAAAACCTAACCCCCAA
Found at i:534540 original size:21 final size:19
Alignment explanation
Indices: 534484--534540 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
534474 GCCCATTAAG
*
534484 CCCAAAAAAAACCTAACCC
1 CCCAAAAAAAAACTAACCC
*
534503 CCAAAAAAAAAACCTAACCCCC
1 CCCAAAAAAAAA-CTAA--CCC
534525 CCCAAAAAAAAACTAA
1 CCCAAAAAAAAACTAA
534541 GAAACCCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 10 0.31
20 4 0.12
21 4 0.12
22 14 0.44
ACGTcount: A:0.58, C:0.37, G:0.00, T:0.05
Consensus pattern (19 bp):
CCCAAAAAAAAACTAACCC
Found at i:535799 original size:23 final size:23
Alignment explanation
Indices: 535741--535804 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
535731 TCATGATTAC
535741 TATATA-TTAGTGTATATTTTTTA
1 TATATATTTA-TGTATATTTTTTA
* *
535764 TTTTATATATATGTATATGTTTTTA
1 -TATATATTTATGTATAT-TTTTTA
535789 -ATATATTTATGTATAT
1 TATATATTTATGTATAT
535805 ACTTATGTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.41
24 12 0.35
25 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (23 bp):
TATATATTTATGTATATTTTTTA
Found at i:535897 original size:30 final size:30
Alignment explanation
Indices: 535842--535918 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
535832 TTTATCCCTA
535842 ATAT-TTATGTATTATATAAATA-TTTTAAT
1 ATATATTATGTA-TATATAAATATTTTTAAT
* * **
535871 ATTATATTATGTATATCTATATATTTTTCGT
1 A-TATATTATGTATATATAAATATTTTTAAT
535902 ATATATTATGTATATAT
1 ATATATTATGTATATAT
535919 GTTTTCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 26 0.65
31 13 0.32
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
ATATATTATGTATATATAAATATTTTTAAT
Found at i:536023 original size:19 final size:19
Alignment explanation
Indices: 535999--536035 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
535989 CTATTTTATA
*
535999 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
536018 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
536036 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:536140 original size:20 final size:18
Alignment explanation
Indices: 536104--536143 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
536094 ATTTCTAATA
*
536104 TATATATTATATGTATTT
1 TATATATTATATATATTT
536122 TATATATTATGTATATATTT
1 TATATATTA--TATATATTT
536142 TA
1 TA
536144 AAGTTATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATATTATATATATTT
Found at i:536433 original size:37 final size:35
Alignment explanation
Indices: 536368--536437 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
536358 TTATATATAG
536368 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
536405 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
536438 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:544950 original size:11 final size:11
Alignment explanation
Indices: 544934--544960 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
544924 TGGTTTTGGA
544934 TTTCTTTCGTC
1 TTTCTTTCGTC
544945 TTTCTTTCGTC
1 TTTCTTTCGTC
544956 TTTCT
1 TTTCT
544961 CCATAGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTCTTTCGTC
Found at i:546244 original size:20 final size:20
Alignment explanation
Indices: 546221--546261 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
546211 AAATCCAAAT
546221 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
* *
546241 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
546261 T
1 T
546262 TAAGAGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:547657 original size:29 final size:29
Alignment explanation
Indices: 547602--547658 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
547592 TAAAATAATG
* *
547602 ATATGTGCAAAAAATATATATATATATAC
1 ATATGTACAAAAAATATACATATATATAC
*
547631 ATATGTACATAAAATATACACTA-ATATA
1 ATATGTACAAAAAATATACA-TATATATA
547659 ATAATAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (29 bp):
ATATGTACAAAAAATATACATATATATAC
Found at i:547828 original size:39 final size:39
Alignment explanation
Indices: 547727--547828 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
547717 TATGGTATTT
* * * *
547727 AAAATATATATATATATATATATGTATATAATAGTATTTA
1 AAAATATATACATA-ATATATATATATATAATAGCATTAA
* * * *
547767 AGAATATATACATAAGAAATATATA-ACTAATGGCATTAA
1 AAAATATATACATAATATATATATATA-TAATAGCATTAA
547806 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
547829 AAATACCTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.02
39 37 0.74
40 12 0.24
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATATATAATAGCATTAA
Found at i:548358 original size:16 final size:15
Alignment explanation
Indices: 548339--548374 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
548329 TTCTTCTTTT
548339 TTTTTTGGGGGTTAGG
1 TTTTTTGGGGG-TAGG
*
548355 TTTTTTTGGGGTAGG
1 TTTTTTGGGGGTAGG
548370 TTTTT
1 TTTTT
548375 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.06, C:0.00, G:0.36, T:0.58
Consensus pattern (15 bp):
TTTTTTGGGGGTAGG
Found at i:548358 original size:17 final size:15
Alignment explanation
Indices: 548338--548374 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
548328 TTTCTTCTTT
548338 TTTTTTTGGGGGTTAGG
1 TTTTTTT-GGGG-TAGG
548355 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
548370 TTTTT
1 TTTTT
548375 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 7 0.35
ACGTcount: A:0.05, C:0.00, G:0.35, T:0.59
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:548387 original size:14 final size:13
Alignment explanation
Indices: 548370--548408 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
548360 TTGGGGTAGG
*
548370 TTTTTCTTTTTCTT
1 TTTTTTTTTTTC-T
548384 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
548397 TTGTTTTTTTTT
1 TT-TTTTTTTTT
548409 TGGGTTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:548393 original size:20 final size:20
Alignment explanation
Indices: 548370--548409 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
548360 TTGGGGTAGG
548370 TTTTTCTTT-TTCTTTTTTTT
1 TTTTTCTTTGTT-TTTTTTTT
548390 TTTTTCTTTGTTTTTTTTTT
1 TTTTTCTTTGTTTTTTTTTT
548410 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (20 bp):
TTTTTCTTTGTTTTTTTTTT
Found at i:549162 original size:88 final size:83
Alignment explanation
Indices: 549055--549632 Score: 299
Period size: 88 Copynumber: 7.0 Consensus size: 83
549045 AACAGACATT
** * *
549055 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
549120 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AAC-TG
* * * ** *
549143 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
549207 GTTGA-TTTTTGAAAAACAG
64 GTTGATTTTTTGAAAAACTG
* * * * ** *** *
549226 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
549287 ATGAGTTGAATTTTTTTG-AAAA---
60 ATGAGTTG-A-TTTTTTGAAAAACTG
** * *
549309 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
549374 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-CTG
* * * * * *
549397 AAAAACAGATTTTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
549462 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAACTG
* *** *** * *
549480 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
549540 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAACTG
* * * * * * *
549557 ATAGA-A-A--TTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
549618 TTGATTTTTTGAAAA
65 TTGATTTTTTGAAAA
549633 CAGAAATTGA
Statistics
Matches: 384, Mismatches: 69, Indels: 84
0.72 0.13 0.16
Matches are distributed among these distances:
76 9 0.02
77 47 0.12
78 2 0.01
79 64 0.17
80 3 0.01
81 11 0.03
82 38 0.10
83 14 0.04
84 41 0.11
85 9 0.02
86 6 0.02
87 19 0.05
88 115 0.30
90 6 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAACTG
Found at i:549259 original size:30 final size:30
Alignment explanation
Indices: 549223--549284 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
549213 TTTTGAAAAA
549223 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
549253 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
549283 CA
1 CA
549285 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:549403 original size:14 final size:14
Alignment explanation
Indices: 549380--549414 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
549370 TGAGTTGATT
549380 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
549393 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
549407 TTTGAAAA
1 TTTGAAAA
549415 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:549604 original size:77 final size:75
Alignment explanation
Indices: 549434--549773 Score: 370
Period size: 72 Copynumber: 4.5 Consensus size: 75
549424 ATGTAACCCG
* * * *
549434 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTG--AAAATACCT
* *
549499 CAGTGTGTGATCTGA
63 CA--GCGTGATCTCA
* *
549514 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
*
549578 GCGCATGAGC-CA
65 GCG--TGATCTCA
* * *
549590 AGGGTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
549654 CGTG-TCTTG
66 CGTGATCTCA
** * * *
549663 AGGCTCAACTCATTTCTCACAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
* *
549726 CGTG-TCCCG
66 CGTGATCTCA
549735 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
549774 TTTTTTTGAA
Statistics
Matches: 224, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
72 65 0.29
73 29 0.13
74 4 0.02
75 23 0.10
76 12 0.05
77 42 0.19
78 3 0.01
79 45 0.20
80 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGATCTCA
Found at i:549715 original size:72 final size:73
Alignment explanation
Indices: 549432--549963 Score: 388
Period size: 73 Copynumber: 6.8 Consensus size: 73
549422 ACATGTAACC
* * * *
549432 CGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG--AAAATAC
* *
549497 CTCAGTGTGTGAT
62 CTCAGCGTGT-CT
* * *
549510 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGC
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
549575 TCAGCGCATGAGC-
63 TCAGCG--TG-TCT
* * *
549588 CAAGGGTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
549653 ACGTGTCT
66 GCGTGTCT
* ** * * *
549661 TGAGGCTCAACTCATTTCTCACAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
549725 GCGTGTCC
66 GCGTGTCT
*
549733 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTTTTGAAATGCAGAAATTGAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--------TTTTTTGAAA-ACAGAAATTG--
** ** *
549798 AAATGGAAATTGAAAATACCTCGACGTGTGAT
55 --A---AAA-T--ACCT-CAGC---GTGT-CT
* * *
549830 CTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTTTGACAACAGAAATTGAAATTACCT
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
549895 CA-CGTGTC-
64 CAGCGTGTCT
* *
549903 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAAAAATTGAAAA
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAA
549964 ACGGAAATTG
Statistics
Matches: 366, Mismatches: 55, Indels: 70
0.75 0.11 0.14
Matches are distributed among these distances:
72 65 0.18
73 72 0.20
74 11 0.03
75 25 0.07
76 10 0.03
77 41 0.11
78 6 0.02
79 50 0.14
80 2 0.01
81 8 0.02
82 10 0.03
83 2 0.01
86 2 0.01
89 2 0.01
90 10 0.03
91 9 0.02
92 2 0.01
93 2 0.01
96 4 0.01
97 1 0.00
98 32 0.09
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (73 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
GCGTGTCT
Found at i:550092 original size:74 final size:75
Alignment explanation
Indices: 549967--550106 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 75
549957 TTGAAAAACG
* *
549967 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
550032 TTTTGACAACA
65 TTTTGACAACA
* * *
550043 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
550107 GAAAAAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 37 0.63
76 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:550098 original size:165 final size:164
Alignment explanation
Indices: 549629--550106 Score: 694
Period size: 164 Copynumber: 2.9 Consensus size: 164
549619 TGATTTTTTG
* * * ** * *
549629 AAAACAGAAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
549692 TGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
* *
549756 ATATGAGTTGATTTTTTTTTTTTTTGAAATGCAGAAATTGA
131 ATATGAGTTGA-------TTTTTTTGAAAGGCAAAAATTGA
* *
549797 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
549862 TGACTTTTTTGACAACAGAAATTGAAATTACCTCA-CGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
549926 AATATGAGTTGATTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTGAAAGGCAAAAATTGA
* * *
549961 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
550026 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
550091 AATATGAGTTGATTTT
130 AATATGAGTTGATTTT
550107 GAAAAAGTAG
Statistics
Matches: 285, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
164 115 0.40
165 45 0.16
168 27 0.09
170 30 0.11
171 40 0.14
172 28 0.10
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (164 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTGAAAGGCAAAAATTGA
Found at i:550295 original size:212 final size:209
Alignment explanation
Indices: 549906--550508 Score: 654
Period size: 212 Copynumber: 2.9 Consensus size: 209
549896 ACGTGTCCTG
* *
549906 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAA--AAATTGAAAAACGGA
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGA---TTTTG-AA--CAACTAAATTG-AAAACAGA
* * * *
549969 AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTTT
59 AATTGAAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
*** * *
550034 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
121 AAAAC-ACAAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
550099 TTGATTTTGAAAAAGTAGAAATTAAA
185 TTGATTTTGAAAAA-CAAAAATTAAA
550125 AGG-TTCAAC-CTACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAAT
1 AGGCTT-AACTC-ACCTCTCGCAATATGAGTTGATT-TTGAACAAC-TAAATTGAAAACAGAAAT
**
550188 TGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACA
62 TGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACA
* * *
550253 CAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTT
127 CAAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
550318 TGAAAAACAAAAATTAAA
192 TGAAAAACAAAAATTAAA
* *
550336 AGGCTTAACTCACCTCTCGCAATATGA---G----T---CAA-T---TT-AAAACATAAACT-AA
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACTAAATTGAAAACAGAAATTGAA
* * * *
550385 AATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-ACAAA
66 AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACACAAA
* * * * *
550449 AATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCACAATATGAGTTGATT
131 AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
550509 AAAACACAAA
Statistics
Matches: 342, Mismatches: 34, Indels: 43
0.82 0.08 0.10
Matches are distributed among these distances:
192 57 0.17
193 55 0.16
194 10 0.03
195 2 0.01
198 1 0.00
200 3 0.01
203 1 0.00
208 1 0.00
211 31 0.09
212 71 0.21
213 4 0.01
214 40 0.12
216 28 0.08
217 9 0.03
218 2 0.01
219 27 0.08
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (209 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACTAAATTGAAAACAGAAATTGAA
AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACACAAA
AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAA
AAACAAAAATTAAA
Found at i:550305 original size:72 final size:71
Alignment explanation
Indices: 550171--550336 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
550161 TGAACAACGT
* * * *
550171 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
550236 GAGTTG
66 GAGTTG
*
550242 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
550307 TGAGTTG
65 TGAGTTG
**
550314 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
550337 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:550429 original size:121 final size:124
Alignment explanation
Indices: 550211--550713 Score: 501
Period size: 121 Copynumber: 4.0 Consensus size: 124
550201 GCGTGACCTG
*
550211 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTGAAAATACCTCAGCG
550276 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * *
550336 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACT-AAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTGAAAATACCTCAGCG
* *
550397 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATT-AAA
** * * * * * * * * *
550457 ATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCACAATATGAGTTGATTAAAACACAAAAAT
1 A-GGCTCAAC---TC---A-CCTC-TCGCA-ATAT--GAGT-TGA---AATTAAAACACAAAAAC
550522 TGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA
50 TGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAA
550587 CAAAAATTAAA
114 CAAAAATTAAA
* * * *
550598 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATT-------TAAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTGAAAATACCTCAGCG
* * * * *
550654 TGTCCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTGAAAACAACAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
550713 A
1 A
550714 ATACCTCAAC
Statistics
Matches: 312, Mismatches: 44, Indels: 54
0.76 0.11 0.13
Matches are distributed among these distances:
115 15 0.05
116 59 0.19
120 12 0.04
121 60 0.19
122 12 0.04
123 10 0.03
124 1 0.00
125 29 0.09
127 1 0.00
128 1 0.00
129 4 0.01
130 3 0.01
131 4 0.01
132 3 0.01
133 4 0.01
134 1 0.00
135 1 0.00
137 2 0.01
139 6 0.02
140 12 0.04
141 60 0.19
142 12 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTGAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:550484 original size:71 final size:71
Alignment explanation
Indices: 550336--550598 Score: 338
Period size: 70 Copynumber: 3.7 Consensus size: 71
550326 AAAAATTAAA
* * * * *
550336 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACT-AAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
550398 GCCCCG
66 GCCCCG
* *
550404 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
* **
550469 GTCTTG
66 GCCCCG
* * * *
550475 AGGCTCAACTCATCTCTCACAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
550538 TGCCCCG
65 TGCCCCG
*
550545 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
550599 GGCTTAACTC
Statistics
Matches: 164, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
68 26 0.16
69 10 0.06
70 65 0.40
71 46 0.28
72 14 0.09
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GCCCCG
Found at i:550552 original size:262 final size:257
Alignment explanation
Indices: 550174--550765 Score: 1031
Period size: 262 Copynumber: 2.3 Consensus size: 257
550164 ACAACGTAAA
* * * * * *
550174 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
550239 TTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
66 TTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
550304 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
129 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
550369 TTAAAACATAAACTAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTT
194 TTAAAAC-T--A--AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTT
550434 GATT
254 GATT
*
550438 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCACAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
550503 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
550568 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
* *
550633 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATT
196 AAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
*
550695 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
550760 TTGATT
66 TTGATT
550766 TTCCTTGAAA
Statistics
Matches: 317, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
257 122 0.38
259 1 0.00
261 1 0.00
262 132 0.42
264 61 0.19
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (257 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
AAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Found at i:555450 original size:46 final size:44
Alignment explanation
Indices: 555391--555505 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
555381 ACAGGACAGA
* *
555391 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
555437 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
555481 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
555506 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:555486 original size:44 final size:45
Alignment explanation
Indices: 555391--555524 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
555381 ACAGGACAGA
* *
555391 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
555437 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
555481 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
555525 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:561590 original size:46 final size:44
Alignment explanation
Indices: 561531--561645 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
561521 ACAGGACAGA
* *
561531 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
561577 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
561621 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
561646 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:561626 original size:44 final size:45
Alignment explanation
Indices: 561531--561664 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
561521 ACAGGACAGA
* *
561531 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
561577 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
561621 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
561665 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:568503 original size:39 final size:37
Alignment explanation
Indices: 568406--568503 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 37
568396 TATGGTATTT
* * * *
568406 AAAATATATATAT-ATATATGTATATAATAGTATTTA
1 AAAATATATACATAATATATATATATAATAGCATTAA
* * * *
568442 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATAT-A-TAATAGCATTAA
568481 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
568504 AAATACCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 11 0.23
37 7 0.15
38 1 0.02
39 29 0.60
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (37 bp):
AAAATATATACATAATATATATATATAATAGCATTAA
Found at i:569033 original size:16 final size:15
Alignment explanation
Indices: 569014--569049 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
569004 TTTCTTCTTT
569014 TTTTTTTGGGGTTAGG
1 TTTTTTTGGGG-TAGG
569030 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
569045 TTTTT
1 TTTTT
569050 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.06, C:0.00, G:0.33, T:0.61
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:569080 original size:15 final size:15
Alignment explanation
Indices: 569045--569080 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
569035 TTGGGGTAGG
*
569045 TTTTTCTTTTTCTTT
1 TTTTTTTTTTTCTTT
569060 TTTTTTTTTTTCTTT
1 TTTTTTTTTTTCTTT
569075 TTTTTT
1 TTTTTT
569081 GGGTTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (15 bp):
TTTTTTTTTTTCTTT
Found at i:574193 original size:2 final size:2
Alignment explanation
Indices: 574186--574217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
574176 AATGATAAGC
574186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
574218 TCCTTGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:588425 original size:16 final size:16
Alignment explanation
Indices: 588404--588435 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
588394 TGGGTCAAGT
588404 TGATTTTGGATCGATC
1 TGATTTTGGATCGATC
588420 TGATTTTGGATCGATC
1 TGATTTTGGATCGATC
588436 AATCTGGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
TGATTTTGGATCGATC
Found at i:589938 original size:30 final size:30
Alignment explanation
Indices: 589877--589937 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
589867 TATAGTCAAC
* *
589877 AAATAATTTAAAATTTATAAAAGTATTAAA
1 AAATAAATTAAAATTTATAAAAGCATTAAA
589907 AAATAAATTAAAATTT-TAAAA-CATTAAA
1 AAATAAATTAAAATTTATAAAAGCATTAAA
589935 AAA
1 AAA
589938 AGCATGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.31
29 5 0.17
30 15 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATAAATTAAAATTTATAAAAGCATTAAA
Found at i:592046 original size:2 final size:2
Alignment explanation
Indices: 592039--592073 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
592029 TGTTGATACC
592039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
592074 CAATTCTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:592261 original size:118 final size:119
Alignment explanation
Indices: 592061--592298 Score: 469
Period size: 118 Copynumber: 2.0 Consensus size: 119
592051 TATATATATA
592061 TATATATATATATCAATTCTAGTAGAAAAACGCTACATCCATTAGTGTGGTACTAACTACCTTGC
1 TATATATATATATCAATTCTAGTAGAAAAACGCTACATCCATTAGTGTGGTACTAACTACCTTGC
592126 TTTAAAATTTTGAGGGGCCAACAAT-AAAATTTTAAAAAATTAAATTATATTTT
66 TTTAAAATTTTGAGGGGCCAACAATAAAAATTTTAAAAAATTAAATTATATTTT
592179 TATATATATATATCAATTCTAGTAGAAAAACGCTACATCCATTAGTGTGGTACTAACTACCTTGC
1 TATATATATATATCAATTCTAGTAGAAAAACGCTACATCCATTAGTGTGGTACTAACTACCTTGC
592244 TTTAAAATTTTGAGGGGCCAACAATAAAAATTTTAAAAAATTAAATTATATTTT
66 TTTAAAATTTTGAGGGGCCAACAATAAAAATTTTAAAAAATTAAATTATATTTT
592298 T
1 T
592299 TATTTTAGAA
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 90 0.76
119 29 0.24
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.37
Consensus pattern (119 bp):
TATATATATATATCAATTCTAGTAGAAAAACGCTACATCCATTAGTGTGGTACTAACTACCTTGC
TTTAAAATTTTGAGGGGCCAACAATAAAAATTTTAAAAAATTAAATTATATTTT
Found at i:594221 original size:12 final size:12
Alignment explanation
Indices: 594204--594238 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
594194 AATGAGAAAT
*
594204 ATGTATGTATGC
1 ATGTATGTATGA
*
594216 ATGTATGCATGA
1 ATGTATGTATGA
594228 ATGTATGTATG
1 ATGTATGTATG
594239 TTATTGGCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTATGTATGA
Found at i:600832 original size:2 final size:2
Alignment explanation
Indices: 600825--600852 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
600815 TCAAAATCTG
600825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
600853 GTATGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:602559 original size:7 final size:7
Alignment explanation
Indices: 602547--602587 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
602537 ACCGCTTGTA
602547 TCAAAAT
1 TCAAAAT
602554 TCAAAAT
1 TCAAAAT
602561 TCAAAAT
1 TCAAAAT
602568 TCAAAAT
1 TCAAAAT
602575 TCAAAAT
1 TCAAAAT
602582 TCAAAA
1 TCAAAA
602588 AATGTATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
TCAAAAT
Found at i:607107 original size:4 final size:4
Alignment explanation
Indices: 607098--607127 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
607088 CCCGCCCCTT
607098 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
607128 AAAGCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:611256 original size:20 final size:20
Alignment explanation
Indices: 611231--611269 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
611221 CGTTTTTAAT
* *
611231 TAAATTGATTTATTTAATAG
1 TAAATTGACTAATTTAATAG
611251 TAAATTGACTAATTTAATA
1 TAAATTGACTAATTTAATA
611270 TGATATCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TAAATTGACTAATTTAATAG
Found at i:613193 original size:41 final size:41
Alignment explanation
Indices: 613137--613220 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
613127 GTCAAATCAA
613137 AATAATAATAATAATAATTTGAACTTAAAGTAACCTTAATT
1 AATAATAATAATAATAATTTGAACTTAAAGTAACCTTAATT
613178 AATAATAATAATAATAATTTGAACTTAAAGTAACCTTAATT
1 AATAATAATAATAATAATTTGAACTTAAAGTAACCTTAATT
613219 AA
1 AA
613221 AAATCAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (41 bp):
AATAATAATAATAATAATTTGAACTTAAAGTAACCTTAATT
Found at i:614818 original size:5 final size:5
Alignment explanation
Indices: 614803--614856 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
614793 TATTAACTTT
* * * *
614803 TTAAGA TTAAA TTAAA TTAAG TTAAA TTTAAA TTCAA TTTAA TCAAA TTAAA
1 TTAA-A TTAAA TTAAA TTAAA TTAAA -TTAAA TTAAA TTAAA TTAAA TTAAA
614855 TT
1 TT
614857 CTAATCGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
5 31 0.77
6 9 0.22
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:614822 original size:16 final size:16
Alignment explanation
Indices: 614803--614836 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
614793 TATTAACTTT
614803 TTAAGATTAAA-TTAAA
1 TTAAG-TTAAATTTAAA
614819 TTAAGTTAAATTTAAA
1 TTAAGTTAAATTTAAA
614835 TT
1 TT
614837 CAATTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TTAAGTTAAATTTAAA
Found at i:614850 original size:21 final size:21
Alignment explanation
Indices: 614808--614857 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
614798 ACTTTTTAAG
*
614808 ATTAAATT-AAATTAAGTTAA
1 ATTAAATTCAAATTAAGTCAA
*
614828 ATTTAAATTCAATTTAA-TCAA
1 A-TTAAATTCAAATTAAGTCAA
614849 ATTAAATTC
1 ATTAAATTC
614858 TAATCGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 11 0.42
22 6 0.23
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTAAATTCAAATTAAGTCAA
Found at i:626790 original size:16 final size:16
Alignment explanation
Indices: 626769--626804 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
626759 TCATTTTGAT
*
626769 TTTTGAGTTTAGATTA
1 TTTTGAGCTTAGATTA
*
626785 TTTTGAGCTTGGATTA
1 TTTTGAGCTTAGATTA
626801 TTTT
1 TTTT
626805 AAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTTGAGCTTAGATTA
Found at i:629637 original size:29 final size:29
Alignment explanation
Indices: 629595--629654 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
629585 TCATAAGATT
*
629595 AAACCTTACTTAACATCAACTGAATTTGA
1 AAACCTTACTTAACATCAACTGAATTCGA
629624 AAACCTTACTTAACATCAACTGAATTCGA
1 AAACCTTACTTAACATCAACTGAATTCGA
629653 AA
1 AA
629655 CTGATGTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (29 bp):
AAACCTTACTTAACATCAACTGAATTCGA
Found at i:635363 original size:18 final size:18
Alignment explanation
Indices: 635331--635370 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
635321 TAATTTTATA
635331 TTTTAATTTGATATTATATT
1 TTTTAATTT-ATATTA-ATT
635351 TTTTAATTT-TATTAATT
1 TTTTAATTTATATTAATT
635368 TTT
1 TTT
635371 CGAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
20 9 0.45
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTAATTTATATTAATT
Found at i:638633 original size:21 final size:21
Alignment explanation
Indices: 638609--638679 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
638599 AATGTGTAAC
638609 ATTTTAAACCCTATTTATAAA
1 ATTTTAAACCCTATTTATAAA
** * * *
638630 ATTTTAATTAATC-ATGTGTAAC
1 ATTTTAA--ACCCTATTTATAAA
638652 ATTTTAAACCCTATTTATAAA
1 ATTTTAAACCCTATTTATAAA
638673 ATTTTAA
1 ATTTTAA
638680 TTAATCACTG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 2 0.05
21 20 0.54
22 13 0.35
23 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTTTAAACCCTATTTATAAA
Found at i:638647 original size:43 final size:43
Alignment explanation
Indices: 638600--638686 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
638590 TTAATGGAAA
638600 ATGTGTAACATTTTAAACCCTATTTATAAAATTTTAATTAATC
1 ATGTGTAACATTTTAAACCCTATTTATAAAATTTTAATTAATC
638643 ATGTGTAACATTTTAAACCCTATTTATAAAATTTTAATTAATC
1 ATGTGTAACATTTTAAACCCTATTTATAAAATTTTAATTAATC
638686 A
1 A
638687 CTGTATTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (43 bp):
ATGTGTAACATTTTAAACCCTATTTATAAAATTTTAATTAATC
Found at i:639234 original size:23 final size:22
Alignment explanation
Indices: 639193--639235 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
639183 TAATTATGTT
*
639193 TTTTTATAAAATTAAATATTGA
1 TTTTTAAAAAATTAAATATTGA
*
639215 TTTTTAAAAAATATATATATT
1 TTTTTAAAAAAT-TAAATATT
639236 TTTTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTAAAAAATTAAATATTGA
Found at i:639239 original size:21 final size:20
Alignment explanation
Indices: 639191--639239 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
639181 TATAATTATG
*
639191 TTTTTTTATAAAATTAAATA
1 TTTTTTTAAAAAATTAAATA
*
639211 TTGATTTTTAAAAAATATATATA
1 TT--TTTTTAAAAAAT-TAAATA
639234 TTTTTT
1 TTTTTT
639240 ACATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 11 0.46
23 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTTTAAAAAATTAAATA
Found at i:639920 original size:19 final size:19
Alignment explanation
Indices: 639892--639930 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
639882 TTACATGTTC
*
639892 TATTTCATATTCAAATTAA
1 TATTTAATATTCAAATTAA
*
639911 TATTTAATATTTAAATTAA
1 TATTTAATATTCAAATTAA
639930 T
1 T
639931 GATTAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAATATTCAAATTAA
Found at i:647367 original size:2 final size:2
Alignment explanation
Indices: 647360--647387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
647350 TAGAATCAGA
647360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
647388 GTAATACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:647749 original size:2 final size:2
Alignment explanation
Indices: 647744--647773 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
647734 CACATTGGAA
647744 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
647774 ACACTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:647941 original size:25 final size:25
Alignment explanation
Indices: 647913--647965 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
647903 ATATTATGTG
*
647913 AAATAATGTATAGAATACA-ATATTA
1 AAAT-ATGTACAGAATACACATATTA
* *
647938 AAATATTTACATAATACACATATTA
1 AAATATGTACAGAATACACATATTA
647963 AAA
1 AAA
647966 ATAACTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATATGTACAGAATACACATATTA
Found at i:647976 original size:25 final size:24
Alignment explanation
Indices: 647926--647978 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
647916 TAATGTATAG
**
647926 AATACAATATTAAAATATTTACAT
1 AATACAATATTAAAATAACTACAT
647950 AATACACATATTAAAAATAACTA-AT
1 AATACA-ATATT-AAAATAACTACAT
647975 AATA
1 AATA
647979 ATATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (24 bp):
AATACAATATTAAAATAACTACAT
Found at i:648750 original size:20 final size:19
Alignment explanation
Indices: 648713--648751 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
648703 TTTTGTGTTA
* *
648713 TTTATTTATTTATTTATAT
1 TTTATTTATTAATATATAT
648732 TTTATGTTATTAATATATAT
1 TTTAT-TTATTAATATATAT
648752 ATGCACTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTTATTAATATATAT
Found at i:649220 original size:16 final size:16
Alignment explanation
Indices: 649199--649270 Score: 78
Period size: 16 Copynumber: 4.5 Consensus size: 16
649189 GGTTTAGTTA
*
649199 GGTTTAATGGGTTTTG
1 GGTTTAGTGGGTTTTG
649215 GGTTTAGTGGGTTTT-
1 GGTTTAGTGGGTTTTG
649230 GG-TTAGTTGGGGTTATTG
1 GGTTTAG-T-GGGTT-TTG
649248 GG-TTAGTGGGTTTTG
1 GGTTTAGTGGGTTTTG
*
649263 GGTCTAGT
1 GGTTTAGT
649271 TGTTGGGCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
14 4 0.08
15 8 0.16
16 28 0.57
17 3 0.06
18 6 0.12
ACGTcount: A:0.10, C:0.01, G:0.42, T:0.47
Consensus pattern (16 bp):
GGTTTAGTGGGTTTTG
Found at i:649254 original size:32 final size:34
Alignment explanation
Indices: 649207--649272 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 34
649197 TAGGTTTAAT
649207 GGGTTTTGGGTTTAGTGGGTTTT-GGT-TAGTTG
1 GGGTTTTGGGTTTAGTGGGTTTTGGGTCTAGTTG
649239 GGGTTATTGGG-TTAGTGGGTTTTGGGTCTAGTTG
1 GGGTT-TTGGGTTTAGTGGGTTTTGGGTCTAGTTG
649273 TTGGGCTCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 17 0.55
33 8 0.26
34 6 0.19
ACGTcount: A:0.08, C:0.02, G:0.44, T:0.47
Consensus pattern (34 bp):
GGGTTTTGGGTTTAGTGGGTTTTGGGTCTAGTTG
Found at i:650642 original size:46 final size:44
Alignment explanation
Indices: 650538--650643 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 44
650528 TGTCTTTGAC
** * * *
650538 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
650582 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
650628 ATGGACTTACATGGCT
1 ATGGACTTACATGGCT
650644 TATTTCTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 33 0.61
46 21 0.39
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:657114 original size:131 final size:131
Alignment explanation
Indices: 656845--657247 Score: 524
Period size: 131 Copynumber: 3.1 Consensus size: 131
656835 TAGAATTTCT
* * *
656845 AAACATGAGTGAAATTCTAAAGGGGATATTCGATTATTTTGAACCAACAGGAAATCGCAAGCCAG
1 AAACATGAGTGAAATTCTAAA-GGGATATTCGATTATTTTGAACAAACGGGAAATCGCAACCCAG
* * *
656910 CACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATCACCTTCGTTTTATAGAATCTTT
65 CACGATAGGGCACGATT-CCCGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGAGTTTTT
656975 A-A
129 AGA
* * * * *
656977 AGACATGGGTGAAATTCTAAAAGAATATTCGATTATTTTGAACGAACGGGAAATCGCAACCCAGC
1 AAACATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACGGGAAATCGCAACCCAGC
* ** * *
657042 ACGATAGTGCACGATTCCCGAATTGCCAAACATCGAGTATTACCTTCATTTTAAAGAGTTTTTAG
66 ACGATAGGGCACGATTCCCGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGAGTTTTTAG
657107 A
131 A
* * * * *
657108 AAACATGAATGAAATT-TCAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAG
1 AAACATGAGTGAAATTCT-AAAGGGATATTCGATTATTTTGAACAAACGGGAAATCGCAACCCAG
* * *
657172 CACGTTAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAG-GATTTT
65 CACGATAGGGCACGATTCC-CGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGAG-TTTT
657236 TAGA
128 TAGA
657240 AAACATGA
1 AAACATGA
657248 ATGATTAAAA
Statistics
Matches: 234, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
130 42 0.18
131 125 0.53
132 67 0.29
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (131 bp):
AAACATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACGGGAAATCGCAACCCAGC
ACGATAGGGCACGATTCCCGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGAGTTTTTAG
A
Found at i:658174 original size:17 final size:17
Alignment explanation
Indices: 658121--658176 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
658111 TGACAAATCA
*
658121 TAAAGTAAAAAATGTTTT
1 TAAAGTAAAAAATG-TAT
* *
658139 TAAAATAGAAAAATCTAT
1 TAAAGTA-AAAAATGTAT
*
658157 TAAAGTAATAAATGTAT
1 TAAAGTAAAAAATGTAT
658174 TAA
1 TAA
658177 TATATATACA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 11 0.35
18 14 0.45
19 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (17 bp):
TAAAGTAAAAAATGTAT
Found at i:660594 original size:10 final size:10
Alignment explanation
Indices: 660579--660610 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
660569 TAAATACATT
660579 TAATTAAAGA
1 TAATTAAAGA
660589 TAATTAAAGA
1 TAATTAAAGA
660599 TAATTAAA-A
1 TAATTAAAGA
660608 TAA
1 TAA
660611 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:660622 original size:19 final size:18
Alignment explanation
Indices: 660598--660641 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
660588 ATAATTAAAG
660598 ATAATTAAAATAAAATCCTA
1 ATAATTAAAAT--AATCCTA
*
660618 A-AATTTAAATAATCCTA
1 ATAATTAAAATAATCCTA
660635 ATAATTA
1 ATAATTA
660642 TCTTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 8 0.38
20 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAAATAATCCTA
Found at i:686024 original size:21 final size:21
Alignment explanation
Indices: 685990--686035 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
685980 TAATATTGAT
*
685990 ATTTTTAAGATTTAATAAAATA
1 ATTTTCAAGATTT-ATAAAATA
*
686012 ATTTTCAAG-TTTATAGAATA
1 ATTTTCAAGATTTATAAAATA
686032 ATTT
1 ATTT
686036 AAAATTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
ATTTTCAAGATTTATAAAATA
Found at i:690637 original size:17 final size:17
Alignment explanation
Indices: 690612--690645 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
690602 ATCAACAAAC
690612 CTACCTTAATTTTAAAT
1 CTACCTTAATTTTAAAT
*
690629 CTACTTTAATTTTAAAT
1 CTACCTTAATTTTAAAT
690646 GAAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
CTACCTTAATTTTAAAT
Found at i:692764 original size:20 final size:20
Alignment explanation
Indices: 692739--692794 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
692729 AGTTTTATAA
* *
692739 TTTATATATTTTTTCTAGAT
1 TTTATATATTATTTCTAAAT
692759 TTTATATA-TATTTCTAAAT
1 TTTATATATTATTTCTAAAT
692778 TTTAATATAATTATTTC
1 TTT-ATAT-ATTATTTC
692795 CATTATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 1 0.03
22 6 0.19
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATATATTATTTCTAAAT
Found at i:693300 original size:31 final size:32
Alignment explanation
Indices: 693262--693324 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
693252 AAAAAACAGA
*
693262 ATTAGCATATTGGCCCCAATG-TTTTAGCAAC
1 ATTAGCATATTAGCCCCAATGTTTTTAGCAAC
693293 ATTAGCATATTAGCCCCAATGTTTTTAGCAAC
1 ATTAGCATATTAGCCCCAATGTTTTTAGCAAC
693325 TTTATGAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (32 bp):
ATTAGCATATTAGCCCCAATGTTTTTAGCAAC
Found at i:698018 original size:48 final size:48
Alignment explanation
Indices: 697952--698046 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
697942 TCATAATTGA
697952 AGCATTGATTGTGCTAGTCCTAATGCTTAAATTTAAGTTCCATCATGT
1 AGCATTGATTGTGCTAGTCCTAATGCTTAAATTTAAGTTCCATCATGT
* *
698000 AGCATTGGTTGTGTTAGTCCTAATGCTTAAATTTAAGTTCCATCATG
1 AGCATTGATTGTGCTAGTCCTAATGCTTAAATTTAAGTTCCATCATG
698047 ATTGAAAGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (48 bp):
AGCATTGATTGTGCTAGTCCTAATGCTTAAATTTAAGTTCCATCATGT
Found at i:699795 original size:2 final size:2
Alignment explanation
Indices: 699788--699823 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
699778 AAAGCTCTAT
699788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
699824 AACTCGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:700298 original size:23 final size:22
Alignment explanation
Indices: 700272--700315 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
700262 TTAATAAATG
*
700272 ATAAAATTATATTTTTACTTCTC
1 ATAAAATTATAATTTTA-TTCTC
*
700295 ATAAATTTATAATTTTATTCT
1 ATAAAATTATAATTTTATTCT
700316 GACCCTCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAAAATTATAATTTTATTCTC
Found at i:701438 original size:56 final size:55
Alignment explanation
Indices: 701372--701530 Score: 203
Period size: 56 Copynumber: 2.8 Consensus size: 55
701362 GTCAGTCATG
701372 GAATTCGATATAGACTTGGGTTTTGTATGTAGAGAATTGTTGATAAGTTGTTCT-T
1 GAATTCGATATAGA-TTGGGTTTTGTATGTAGAGAATTGTTGATAAGTTGTTCTAT
* *
701427 CGAATTCGATATAGATTCGGGTTTTATATGTAGAGAATTGTTGATATGTTGTTCTAT
1 -GAATTCGATATAGATT-GGGTTTTGTATGTAGAGAATTGTTGATAAGTTGTTCTAT
* * * *
701484 GAATTCAGATATAGAATCGGTTTTTTGTATGTGGATAATTGTTGATA
1 GAATTC-GATATAG-ATTGG-GTTTTGTATGTAGAGAATTGTTGATA
701531 TGATATGATA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
55 2 0.02
56 55 0.60
57 10 0.11
58 24 0.26
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (55 bp):
GAATTCGATATAGATTGGGTTTTGTATGTAGAGAATTGTTGATAAGTTGTTCTAT
Found at i:710422 original size:7 final size:7
Alignment explanation
Indices: 710410--710441 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
710400 ACTGTAAAAC
710410 AAAATTG
1 AAAATTG
710417 AAAATTG
1 AAAATTG
710424 -AAATTG
1 AAAATTG
710430 -AAATTG
1 AAAATTG
710436 AAAATT
1 AAAATT
710442 CTTTTTGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (7 bp):
AAAATTG
Found at i:713487 original size:22 final size:22
Alignment explanation
Indices: 713439--713481 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
713429 ATAATAATAA
*
713439 TAAAATAGTAGCAACATAGTGG
1 TAAAATAGTAGCAAAATAGTGG
*
713461 TAAAATTGTAGCAAAATAGTG
1 TAAAATAGTAGCAAAATAGTG
713482 AGAAAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAGTGG
Found at i:713527 original size:22 final size:22
Alignment explanation
Indices: 713484--713529 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
713474 AAATAGTGAG
* *
713484 AAAACAATAAGAAAATAGCAAC
1 AAAACAATAAGAAAAAAACAAC
713506 AAAACAATAA-AAAAGAAACAAC
1 AAAACAATAAGAAAA-AAACAAC
713528 AA
1 AA
713530 GAAAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.74, C:0.13, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAACAATAAGAAAAAAACAAC
Found at i:715411 original size:7 final size:7
Alignment explanation
Indices: 715399--715424 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
715389 ACAAAAATTG
715399 CTTGTCA
1 CTTGTCA
715406 CTTGTCA
1 CTTGTCA
715413 CTTGTCA
1 CTTGTCA
715420 CTTGT
1 CTTGT
715425 AGCCAAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.46
Consensus pattern (7 bp):
CTTGTCA
Found at i:715467 original size:31 final size:31
Alignment explanation
Indices: 715430--715631 Score: 269
Period size: 31 Copynumber: 6.5 Consensus size: 31
715420 CTTGTAGCCA
* *
715430 AAGCTACCACTATTCATTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** * *
715461 GTGCTACCATTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* *
715492 GAGCTACCACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* **
715523 AAGCTACCACTTTTCACTGATTAGGTAGAAG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
*
715554 AAGCTACCACTTTTCACTGATCAGGTAGTTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* * *
715585 AAACTACCGCTTTTCATTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
715616 AAGCTACCACTTTTCA
1 AAGCTACCACTTTTCA
715632 GTTGTCATTT
Statistics
Matches: 150, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 150 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:715715 original size:50 final size:50
Alignment explanation
Indices: 715609--715785 Score: 230
Period size: 50 Copynumber: 3.5 Consensus size: 50
715599 CATTGATCAG
* * * * * *
715609 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCC-TTAATCAGATAAGT
*
715660 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
* * * *
715710 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
715760 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
715786 GTTTCCATGG
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 88 0.79
51 23 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
Found at i:718819 original size:79 final size:77
Alignment explanation
Indices: 718725--718883 Score: 237
Period size: 79 Copynumber: 2.0 Consensus size: 77
718715 TTTAAAAGTA
* * *
718725 CTGCACATTGAATTGCTTTGGAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGTGAGAGCA
1 CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACA--TGTGAGAGCA
718790 CCAGTCCCTTCTGC
64 CCAGTCCCTTCTGC
* * *
718804 CTGCACATTAAATTGCTTCGAAAAGTGAACTATGCAGAGAAATTTTAATTACATGTGAGTGGACC
1 CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGCACC
*
718869 ATTCCCTTCTGC
66 AGTCCCTTCTGC
718881 CTG
1 CTG
718884 TAATTCTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 24 0.33
79 49 0.67
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (77 bp):
CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGCACC
AGTCCCTTCTGC
Found at i:719258 original size:48 final size:49
Alignment explanation
Indices: 719175--719268 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 49
719165 TAAATAATTA
* * * *
719175 AATACTCTTAAAATTACTTGTACACTTTCACATTGT-TGTAAATTGTTT
1 AATACTCTTAAAATCACTTGTACACTATCAAATTGTATATAAATTGTTT
* *
719223 AATACTCTTAAAATCATTTGTATA-TCATCAAATTGTATATAAATTG
1 AATACTCTTAAAATCACTTGTACACT-ATCAAATTGTATATAAATTG
719269 ATTCAATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.03
48 29 0.76
49 8 0.21
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (49 bp):
AATACTCTTAAAATCACTTGTACACTATCAAATTGTATATAAATTGTTT
Found at i:725048 original size:30 final size:29
Alignment explanation
Indices: 725009--725094 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 29
724999 TCTCACAAAA
*
725009 TTTTTAAAAATTTTAATTAAACCCT-AAT
1 TTTTTAAAAATTTTAATTAAACCCTAAAG
* *
725037 TCTTTTAAAAAATAATCTCATTAAACTCCTAAAG
1 T-TTTT-AAAAAT--TTTAATTAAAC-CCTAAAG
*
725071 TTTTTGAAAATTTTAATTAAACCC
1 TTTTTAAAAATTTTAATTAAACCC
725095 CCTAAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
28 1 0.02
29 6 0.13
30 15 0.33
32 14 0.30
33 7 0.15
34 3 0.07
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (29 bp):
TTTTTAAAAATTTTAATTAAACCCTAAAG
Found at i:729085 original size:31 final size:30
Alignment explanation
Indices: 729022--729085 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
729012 TTGATACTTA
* **
729022 AGTTTGCTTTAATGTTTAATTTGGTATTTG
1 AGTTTGCTTTAATATTTAATTTGGTACCTG
*
729052 AGTTTGACTTTAATATTTTATTTGGTACCTG
1 AGTTTG-CTTTAATATTTAATTTGGTACCTG
729083 AGT
1 AGT
729086 GTTTTTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (30 bp):
AGTTTGCTTTAATATTTAATTTGGTACCTG
Found at i:734156 original size:42 final size:42
Alignment explanation
Indices: 733978--734149 Score: 245
Period size: 42 Copynumber: 4.1 Consensus size: 42
733968 GTGAAGGAGC
* * * **
733978 AGATTCAAAATTGTCGACGTCGACGGCGAAGTCGCCTCGATA
1 AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
* * ** *
734020 AGATTCAACATCGTCGACGTCAACGGGGACGTCGCCTTGAAA
1 AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
*
734062 AGATTCAACATCGTCGACGTCGACGGGGAAATCGCCGAGATA
1 AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
734104 AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
1 AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
734146 AGAT
1 AGAT
734150 CGAACATTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 116 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.19
Consensus pattern (42 bp):
AGATTCAACATCGTCGACGTCGACGGGGAAGTCGCCGAGATA
Found at i:734233 original size:9 final size:9
Alignment explanation
Indices: 734219--734243 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
734209 GCAAAGAGCA
734219 AAGATGATG
1 AAGATGATG
734228 AAGATGATG
1 AAGATGATG
734237 AAGATGA
1 AAGATGA
734244 AAACAGGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (9 bp):
AAGATGATG
Found at i:739836 original size:36 final size:36
Alignment explanation
Indices: 739604--739829 Score: 308
Period size: 36 Copynumber: 6.1 Consensus size: 36
739594 GTGAAGGAAC
*
739604 AGATTCAACATCGTCGACGGGGAAGTCGCCTCGATA
1 AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
*
739640 AGATTCAACATCGTCGATGTCGACGGAGAAGTCGCCTCGATA
1 AGATTCAACA---TC-A--TCGACGGGGAAGTCGCCTCGATA
*
739682 AGATTCAACATCATCGACGGGGAAGTCTCCTCGATA
1 AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
* *
739718 AGATTCAACGTCATCGACGGGGAAGTCGCCTGGATA
1 AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
*
739754 AGATTCAACATCGTCGACGGGGAAGTCGCCTCGATA
1 AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
* * * *
739790 AGATTCAACATCATCGACTGGAAAGTAGCCCCGATA
1 AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
739826 AGAT
1 AGAT
739830 CGAACATTGT
Statistics
Matches: 169, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
36 132 0.78
38 1 0.01
39 4 0.02
42 32 0.19
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (36 bp):
AGATTCAACATCATCGACGGGGAAGTCGCCTCGATA
Found at i:739913 original size:9 final size:9
Alignment explanation
Indices: 739899--739923 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
739889 GCAAAGAGCA
739899 AAGATGATG
1 AAGATGATG
739908 AAGATGATG
1 AAGATGATG
739917 AAGATGA
1 AAGATGA
739924 AAATAGGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (9 bp):
AAGATGATG
Found at i:744562 original size:16 final size:17
Alignment explanation
Indices: 744533--744566 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
744523 TTTAACCCCC
*
744533 TTTAGAATTTATAAAAA
1 TTTAGAATTAATAAAAA
744550 TTTA-AATTAATAAAAA
1 TTTAGAATTAATAAAAA
744566 T
1 T
744567 AAAATTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAGAATTAATAAAAA
Done.