Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011463.1 Kokia drynarioides strain JFW-HI SEQ_126447, whole genome shotgun sequence
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: 338791
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 497 characters in sequence are not A, C, G, or T
Found at i:613 original size:14 final size:14
Alignment explanation
Indices: 580--613 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
570 TAAAGCAATT
*
580 TTTTTTCTTTTGTA
1 TTTTTTCATTTGTA
*
594 ATTTTTCATTTGTA
1 TTTTTTCATTTGTA
608 TTTTTT
1 TTTTTT
614 GCAATGAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (14 bp):
TTTTTTCATTTGTA
Found at i:7407 original size:51 final size:51
Alignment explanation
Indices: 7329--7610 Score: 374
Period size: 51 Copynumber: 5.5 Consensus size: 51
7319 TAGACGAAAG
* * * * * *
7329 GGTCCGATGACAAACTATCATCGTGAGTGAAAAAATCCTTTATGGATCAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTGAAAGAATCCTTTATGGATTAAA
* *
7380 GCTCCGATGACTAAATGTCATCGTGAGT-AAATG-AT-CTTGTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTGAAA-GAATCCTT-TATGGATTAAA
* *
7430 GGCCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTGAAAGAATCCTTTATGGATTAAA
* * *
7481 GGTCCGATGACTAAGTGTCATTGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTGAAAGAATCCTTTATGGATTAAA
*
7532 GGTCCGATGACTAAGTGTCATCGTGAGT-AAATGAATCCTGTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTGAAA-GAATCCTTTATGGATTAAA
*
7583 GGTCCGATGACTAAGTGTCATCATGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
7611 TTATAGATTC
Statistics
Matches: 206, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
49 3 0.01
50 42 0.20
51 158 0.77
52 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTGAAAGAATCCTTTATGGATTAAA
Found at i:9236 original size:29 final size:28
Alignment explanation
Indices: 9204--9266 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
9194 TTGAAGAATA
9204 TAGGGTCAAAACATAATTTT-AGAAAAGTT
1 TAGGGT-AAAACATAATTTTAAG-AAAGTT
**
9233 TAGGGGTAAAATGTAATTTTAAGAAAGTT
1 TA-GGGTAAAACATAATTTTAAGAAAGTT
9262 T-GGGT
1 TAGGGT
9267 TCTAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 4 0.13
29 20 0.67
30 6 0.20
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (28 bp):
TAGGGTAAAACATAATTTTAAGAAAGTT
Found at i:10051 original size:19 final size:16
Alignment explanation
Indices: 10011--10057 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 16
10001 TTAAAGAAGG
10011 TTTTTTC-TTTTTTTT
1 TTTTTTCGTTTTTTTT
10026 TTTTTTCGTTTTTTTT
1 TTTTTTCGTTTTTTTT
10042 AATTTGTTTCGTTTTT
1 --TTT-TTTCGTTTTT
10058 ACCCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
18 3 0.11
19 10 0.36
ACGTcount: A:0.04, C:0.06, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTCGTTTTTTTT
Found at i:11377 original size:23 final size:23
Alignment explanation
Indices: 11351--11408 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
11341 TGACGTGGCA
*
11351 TCCAATCAGCAGCTTCTAGAAGG
1 TCCAATCAGCAACTTCTAGAAGG
* *
11374 TCCAATCAGTAACTTCTAGAAAG
1 TCCAATCAGCAACTTCTAGAAGG
* *
11397 TCTAGTCAGCAA
1 TCCAATCAGCAA
11409 GGTTGGACGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (23 bp):
TCCAATCAGCAACTTCTAGAAGG
Found at i:17052 original size:9 final size:9
Alignment explanation
Indices: 17038--17071 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
17028 CATGAAGTCA
17038 AAGTCATTG
1 AAGTCATTG
17047 AAGTCATTG
1 AAGTCATTG
*
17056 AAGTCATTA
1 AAGTCATTG
17065 AAGTCAT
1 AAGTCAT
17072 ATAATGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (9 bp):
AAGTCATTG
Found at i:24902 original size:6 final size:6
Alignment explanation
Indices: 24893--24923 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
24883 AGGTACTGGT
24893 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC A
1 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC A
24924 ATGTGGATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
ATTGGC
Found at i:24949 original size:30 final size:30
Alignment explanation
Indices: 24913--24971 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
24903 GCATTGGCAT
*
24913 TGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCAATATGGATGGATCTCTCTG
*
24943 TGGCATTGGCAATATGGATGGTTCTCTCT
1 TGGCATTGGCAATATGGATGGATCTCTCT
24972 ATGATTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.36
Consensus pattern (30 bp):
TGGCATTGGCAATATGGATGGATCTCTCTG
Found at i:27375 original size:99 final size:99
Alignment explanation
Indices: 27196--27496 Score: 372
Period size: 99 Copynumber: 3.0 Consensus size: 99
27186 AGCTCATCTT
* * * * * *
27196 GGAGGCTACTTCCAACATGACCATTGAGTTTATTTACTTGAACTGGGTTAACCCTACGCTCCAAG
1 GGAGGCTACTTCCAATATGACTATTGAGATTATTTGCTTGAACTGAGTTAACCCTACGCTCCGAG
* * * *
27261 TACATCGGTTTAGCTGTATAAACTCCATTTTCTG
66 TAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
* * * * * *
27295 GGTGGCTACTTCCAGTATGACTATTGAGATTATTGGCTTCAACTAAGTTAACCCTACGTTCCGAG
1 GGAGGCTACTTCCAATATGACTATTGAGATTATTTGCTTGAACTGAGTTAACCCTACGCTCCGAG
27360 TAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
66 TAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
* *
27394 GGAGGCTACTTCCAATATGAATATT-AAATTGATTTGCTTGAACTGAGTTAACCCTACGCTCCGA
1 GGAGGCTACTTCCAATATGACTATTGAGATT-ATTTGCTTGAACTGAGTTAACCCTACGCTCCGA
* * * *
27458 GTAAACCGGTTCA-ATCCTATAAACTCCATCTTTTG
65 GTAAACCGGTTGAGCT-GTATAAACTCCATCTTCTG
27493 GGAG
1 GGAG
27497 CATCTCTTCC
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
98 5 0.03
99 167 0.97
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (99 bp):
GGAGGCTACTTCCAATATGACTATTGAGATTATTTGCTTGAACTGAGTTAACCCTACGCTCCGAG
TAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
Found at i:28031 original size:72 final size:72
Alignment explanation
Indices: 27945--28520 Score: 928
Period size: 72 Copynumber: 8.0 Consensus size: 72
27935 TCGGCGTTCA
* * *
27945 TTGGATCGAGTTGAGTCTGATCATTTG-TTCTTGCTAATGGAGGTGGAAGTTCCACTCCTACATC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTTC-TGCCAATGGAGGTGGAAGTTCCACTCCTACATC
28009 CACCTGAG
65 CACCTGAG
* * * * *
28017 TTGGATCGAGTTGAGTCTGTTCACTTGTTGT-GGCTAATGGAGGTGGAAGTTCCACTCCTGCATC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTT-TCTGCCAATGGAGGTGGAAGTTCCACTCCTACATC
28081 CACCTGAG
65 CACCTGAG
*
28089 TTGGATCGGGTTGAGTCTGCTCATTTGTTGT-T-CCTAATGGAGGTGGAAGTTCCACTCCTACAT
1 TTGGATCGGGTTGAGTCTGTTCATTTGTT-TCTGCC-AATGGAGGTGGAAGTTCCACTCCTACAT
28152 CCACCTGAG
64 CCACCTGAG
*
28161 TTGGATCGGGTTGAGTCCGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
28226 ACCTGAG
66 ACCTGAG
28233 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
28298 ACCTGAG
66 ACCTGAG
* *
28305 TTGGATCGGATTGAGTCTGTTCATCTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
28370 ACCTGAG
66 ACCTGAG
*
28377 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCTTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
28442 ACCTGAG
66 ACCTGAG
* * *
28449 TTGGATCGGGTTGAGTCTGCTCATTTGTTGT-TTCTAATGGAGGTGGAAGTTCCACTCCTACATC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTT-TCTGCCAATGGAGGTGGAAGTTCCACTCCTACATC
28513 CACCTGAG
65 CACCTGAG
28521 ATGGTTTAGG
Statistics
Matches: 476, Mismatches: 22, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
71 2 0.00
72 469 0.99
73 4 0.01
74 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (72 bp):
TTGGATCGGGTTGAGTCTGTTCATTTGTTTCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
ACCTGAG
Found at i:42487 original size:88 final size:88
Alignment explanation
Indices: 42338--42513 Score: 307
Period size: 88 Copynumber: 2.0 Consensus size: 88
42328 TTGTTTGCAC
* * *
42338 TTGATGAGGAGTTGAAGTATTACCAGTTTTTTGCATTTTAGTGTGCATAAAGCTCATTGATGACA
1 TTGATGAGGAGTTGAAGTATTACCAGTTTTGTGCATTTTAGTGTGCATAAAGATAATTGATGACA
42403 AAGCCTCCATGCCCTAAAGATCT
66 AAGCCTCCATGCCCTAAAGATCT
*
42426 TTGATGAGGAGTTGAAGTATTACCAGTTTTGTGCATTTTAGTGTGCATATAGATAATTGATGACA
1 TTGATGAGGAGTTGAAGTATTACCAGTTTTGTGCATTTTAGTGTGCATAAAGATAATTGATGACA
*
42491 AAGCCTCTATGCCCTAAAGATCT
66 AAGCCTCCATGCCCTAAAGATCT
42514 GGGATATCAC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (88 bp):
TTGATGAGGAGTTGAAGTATTACCAGTTTTGTGCATTTTAGTGTGCATAAAGATAATTGATGACA
AAGCCTCCATGCCCTAAAGATCT
Found at i:43468 original size:6 final size:6
Alignment explanation
Indices: 43459--43494 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
43449 GGTATTGACG
43459 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA
1 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA
43495 ATGTGGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TTGGCA
Found at i:43518 original size:30 final size:30
Alignment explanation
Indices: 43484--43656 Score: 220
Period size: 30 Copynumber: 5.4 Consensus size: 30
43474 GCATTGGCAT
43484 TGGCATTGGCAATGTGGATGGATCTCTCTGTGG
1 TGGCATTGGCAATGTGGATGGATCTCTC--T-G
43517 CATTGGCATTGGCAATGTGGATGGATCTCTCTG
1 ---TGGCATTGGCAATGTGGATGGATCTCTCTG
*
43550 TGGCATTGGCAATATGGATGGATCTCTCTG
1 TGGCATTGGCAATGTGGATGGATCTCTCTG
43580 TGGCATTGGCAATGTGGATGGATCTCTCCGTGG
1 TGGCATTGGCAATGTGGATGGATCTCT-C-T-G
*
43613 CATTGGCATTGGCAATGTGGATGGATCTCTCCG
1 ---TGGCATTGGCAATGTGGATGGATCTCTCTG
43646 TGGCATTGGCA
1 TGGCATTGGCA
43657 TTGGCATTGG
Statistics
Matches: 128, Mismatches: 3, Indels: 18
0.86 0.02 0.12
Matches are distributed among these distances:
30 66 0.52
31 1 0.01
32 1 0.01
33 3 0.02
34 1 0.01
35 1 0.01
36 55 0.43
ACGTcount: A:0.17, C:0.18, G:0.33, T:0.32
Consensus pattern (30 bp):
TGGCATTGGCAATGTGGATGGATCTCTCTG
Found at i:43525 original size:36 final size:36
Alignment explanation
Indices: 43478--43764 Score: 349
Period size: 36 Copynumber: 8.3 Consensus size: 36
43468 GCATTGGCAT
43478 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
43514 TGGCATTGGCATTGGCAATGTGGATGGATCTCTC--
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
*
43548 T-G---TGGCATTGGCAATATGGATGGATCTCTC--
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
*
43578 T-G---TGGCATTGGCAATGTGGATGGATCTCTCCG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
43610 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCCGTGG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCT-C-T-G
* *
43649 CATTGGCATTGGCATTGGTAATATGGATGGATCTCTCTG
1 ---TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
*
43688 TGGCATTGGCATTGACAATGTGGATGGATCTCTC--
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
43722 T-G---TGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
43754 TGGCATTGGCA
1 TGGCATTGGCA
43765 ATGTGGACGG
Statistics
Matches: 224, Mismatches: 9, Indels: 36
0.83 0.03 0.13
Matches are distributed among these distances:
30 83 0.37
32 2 0.01
33 4 0.02
34 2 0.01
36 97 0.43
37 1 0.00
39 2 0.01
40 1 0.00
41 1 0.00
42 31 0.14
ACGTcount: A:0.18, C:0.17, G:0.32, T:0.33
Consensus pattern (36 bp):
TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
Found at i:43568 original size:66 final size:61
Alignment explanation
Indices: 43484--43782 Score: 287
Period size: 66 Copynumber: 4.5 Consensus size: 61
43474 GCATTGGCAT
43484 TGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGCATTGGCAATGTGGATGGATCTCTCT
1 TGGCATTGGCAATGTGGATGGATCTCTCT-T-G---TGGCATTGGCAATGTGGATGGATCTCTCT
43549 G
61 G
*
43550 TGGCATTGGCAATATGGATGGATCTCTC-TGTGGCATTGGCAATGTGGATGGATCTCTCCGTGG
1 TGGCATTGGCAATGTGGATGGATCTCTCTTGTGGCATTGGCAATGTGGATGGATCTCT-C-T-G
* *
43613 CATTGGCATTGGCAATGTGGATGGATCTCTCCGTGGCATTGGCATTGGCATTGGTAATATGGATG
1 ---TGGCATTGGCAATGTGGATGGA--TCT-C-T--C-TT-G---TGGCATTGGCAATGTGGATG
43678 GATCTCTCTG
52 GATCTCTCTG
43688 TGGCATTGGCATTGACAATGTGGATGGATCTCTC-TGTGGCATTGGCAATGTGGATGGATCTCTC
1 TGGCATT-G----G-CAATGTGGATGGATCTCTCTTGTGGCATTGGCAATGTGGATGGATCTCTC
43752 TG
60 TG
* *
43754 TGGCATTGGCAATGTGGACGGTTCTCTCT
1 TGGCATTGGCAATGTGGATGGATCTCTCT
43783 ATGATTATGA
Statistics
Matches: 200, Mismatches: 8, Indels: 55
0.76 0.03 0.21
Matches are distributed among these distances:
60 44 0.22
61 2 0.01
62 1 0.00
63 2 0.01
64 1 0.00
65 1 0.00
66 83 0.41
68 3 0.01
69 2 0.01
70 2 0.01
72 9 0.05
73 1 0.00
74 2 0.01
75 3 0.01
76 4 0.02
77 2 0.01
78 38 0.19
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.33
Consensus pattern (61 bp):
TGGCATTGGCAATGTGGATGGATCTCTCTTGTGGCATTGGCAATGTGGATGGATCTCTCTG
Found at i:43694 original size:30 final size:30
Alignment explanation
Indices: 43658--43782 Score: 160
Period size: 30 Copynumber: 4.0 Consensus size: 30
43648 GCATTGGCAT
* *
43658 TGGCATTGGTAATATGGATGGATCTCTCTG
1 TGGCATTGGCAATGTGGATGGATCTCTCTG
43688 TGGCATTGGCATTGACAATGTGGATGGATCTCTCTG
1 TGGCATT-G----G-CAATGTGGATGGATCTCTCTG
43724 TGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCAATGTGGATGGATCTCTCTG
* *
43754 TGGCATTGGCAATGTGGACGGTTCTCTCT
1 TGGCATTGGCAATGTGGATGGATCTCTCT
43783 ATGATTATGA
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
30 55 0.65
31 2 0.02
35 2 0.02
36 26 0.31
ACGTcount: A:0.18, C:0.17, G:0.31, T:0.34
Consensus pattern (30 bp):
TGGCATTGGCAATGTGGATGGATCTCTCTG
Found at i:46124 original size:99 final size:99
Alignment explanation
Indices: 45950--46132 Score: 226
Period size: 99 Copynumber: 1.8 Consensus size: 99
45940 AGCTCATCTC
* * * * * *
45950 GGAGGCTACTTTCAAGATGGCCATTGGGTTTATTTGCTTCAACTGAGTTATCCCTTCTCTCCAAG
1 GGAGGCTACTTCCAAGATGACCATTGAGATTATTGGCTTCAACTGAGTTATACCTTCTCTCCAAG
*
46015 TAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
66 GAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
* * *
46049 GGAGGCTACTTCCAATATGACTATTGAGATTATTGGCTTTAACTGAGTTA-ACCTTACGT-TCCA
1 GGAGGCTACTTCCAAGATGACCATTGAGATTATTGGCTTCAACTGAGTTATACCTT-C-TCTCCA
* *
46112 AGGAAACTGGTTGAGTTGTAT
64 AGGAAACCGGTTGAGCTGTAT
46133 TGAATAGATT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
98 4 0.06
99 65 0.93
100 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (99 bp):
GGAGGCTACTTCCAAGATGACCATTGAGATTATTGGCTTCAACTGAGTTATACCTTCTCTCCAAG
GAAACCGGTTGAGCTGTATAAACTCCATCTTCTG
Found at i:49336 original size:6 final size:6
Alignment explanation
Indices: 49320--49352 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
49310 GAGAAGTAAT
*
49320 TTAAAA ATAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA
49353 GGAGGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:50125 original size:20 final size:20
Alignment explanation
Indices: 50099--50143 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
50089 AATGTGAGAT
*
50099 TTTTTTATAATTTTAATATTA
1 TTTTTAATAATTTTAAT-TTA
*
50120 TTTTTAATAATTTTGATTTA
1 TTTTTAATAATTTTAATTTA
50140 TTTT
1 TTTT
50144 ACATGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTAATAATTTTAATTTA
Found at i:51704 original size:16 final size:17
Alignment explanation
Indices: 51683--51718 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
51673 GGAATAAAAA
51683 ATTAATTATA-AAATTG
1 ATTAATTATATAAATTG
*
51699 ATTAATTATATGAATTG
1 ATTAATTATATAAATTG
51716 ATT
1 ATT
51719 TAAAGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
ATTAATTATATAAATTG
Found at i:53473 original size:335 final size:336
Alignment explanation
Indices: 52754--53532 Score: 935
Period size: 335 Copynumber: 2.3 Consensus size: 336
52744 ATTTTTTTTC
* * ** * * * *
52754 CCTTTAAAGAAGAGGGAGAGAATCT-ATGGCCAATTGAACTAAAATTAAAGTGAAAATTATAATC
1 CCTTTAGAGAAGAGGGAGAGTATCTGA-CCCCAATTGAATTAAAATTAAGGTGAAGATTATGATC
* * * * *
52818 ATATCTATATCGAATGAATGATACGC-TT-TTAGATATGAAAAACATAATCTTTGTTTCAGATAA
65 GTATCTATATCGAATGAATG--ACGCGTTCTTAGATATGAAAGACATAATCATTATTTCAGACAA
* * *
52881 AGTATGACATATAAAAAAAGAAAGATTTGAATTAATTACATCGAATCATCCAAAACTTTTTTTCA
128 AGTATGACATATAAAAAAAGAAAGATTTGAATTAACTACATCGAATCACCCAAAACTTCTTTTCA
* * * * *
52946 CTTTACTCAATAAAACCAGAATCAGTAATGGGTACAACTATTGTATCACTATCCAACAAATGACA
193 CTTTACTCAATAAAACCAGAATCAATAATGGGGACAACGATTGTACCACCATCCAACAAATGACA
* ** *
53011 CGTTCTCGGATATGAGCAATATAATTGTAATTTTGTACAGATACATCATACATCGATCATCTTTC
258 CGTTCTCAGATATGAGCAATATAACCGTAATTTTGTACAGATACACCATACATCGATCATCTTTC
53076 TTGTTTTAAATCAT
323 TTGTTTTAAATCAT
* * *
53090 CCTTTAGATAAGAGGGAGAGTATTTGTCCCCAATTGAATTAAAATTAAGGTGAAGATTATGATCG
1 CCTTTAGAGAAGAGGGAGAGTATCTGACCCCAATTGAATTAAAATTAAGGTGAAGATTATGATCG
* * *
53155 TATCTATATCGAATGAATGGCGCGTTCTTAAATCTGAAAGACATAATCATTATTTCAGACAAAGT
66 TATCTATATCGAATGAATGACGCGTTCTTAGATATGAAAGACATAATCATTATTTCAGACAAAGT
** * *
53220 ATGACATATGGAGAAAGAAATATTTGAATTAACTACATCGAATCACCCAAAAC-TCTTTTCAC-T
131 ATGACATATAAAAAAAGAAAGATTTGAATTAACTACATCGAATCACCCAAAACTTCTTTTCACTT
* * * * * * *
53283 TACCTCAACT-GAACCGGAATCAATACTGGGGACAACGATTTTCCCACCATCCAACACATGACAT
196 TA-CTCAA-TAAAACCAGAATCAATAATGGGGACAACGATTGTACCACCATCCAACAAATGACAC
* * * * * * *
53347 GTTTTCATATATGAGCGATGTAACCGTAATTTTGTACATATACACCATACATTGATTATCTTTCT
259 GTTCTCAGATATGAGCAATATAACCGTAATTTTGTACAGATACACCATACATCGATCATCTTTCT
53412 TGTTTTAAATCAT
324 TGTTTTAAATCAT
* * * *
53425 CCTTTAGAGAAGA-GGA-AGTTAATCTGACTCCAATTGAATTAAAATTAAGCTGAAGGTTACGAT
1 CCTTTAGAGAAGAGGGAGAG-T-ATCTGACCCCAATTGAATTAAAATTAAGGTGAAGATTATGAT
* * *
53488 CGTATCTATATTGAACGAATGACACGTTCTTAGATATGAAAGACA
64 CGTATCTATATCGAATGAATGACGCGTTCTTAGATATGAAAGACA
53533 ACTGTTATTC
Statistics
Matches: 374, Mismatches: 62, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
333 2 0.01
334 10 0.03
335 211 0.56
336 151 0.40
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (336 bp):
CCTTTAGAGAAGAGGGAGAGTATCTGACCCCAATTGAATTAAAATTAAGGTGAAGATTATGATCG
TATCTATATCGAATGAATGACGCGTTCTTAGATATGAAAGACATAATCATTATTTCAGACAAAGT
ATGACATATAAAAAAAGAAAGATTTGAATTAACTACATCGAATCACCCAAAACTTCTTTTCACTT
TACTCAATAAAACCAGAATCAATAATGGGGACAACGATTGTACCACCATCCAACAAATGACACGT
TCTCAGATATGAGCAATATAACCGTAATTTTGTACAGATACACCATACATCGATCATCTTTCTTG
TTTTAAATCAT
Found at i:55632 original size:17 final size:19
Alignment explanation
Indices: 55594--55632 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
55584 TTAATTCGAG
55594 TTTTGTTTAAAATAAATAA
1 TTTTGTTTAAAATAAATAA
*
55613 TTTT-TTTAAAA-AAATTA
1 TTTTGTTTAAAATAAATAA
55630 TTT
1 TTT
55633 ACTTCATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTGTTTAAAATAAATAA
Found at i:56100 original size:31 final size:29
Alignment explanation
Indices: 56045--56124 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
56035 ATATCAAAAT
* *
56045 TATACATGAATTATGATTGAATATACAATTG
1 TATACATGAATTTTGATTTAATAT--AATTG
* * *
56076 TATATATGAATTTTGATTTTATATAATTT
1 TATACATGAATTTTGATTTAATATAATTG
56105 TATACATGAAATTTTGATTT
1 TATACATG-AATTTTGATTT
56125 GATCCAATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.26
30 11 0.26
31 20 0.48
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.49
Consensus pattern (29 bp):
TATACATGAATTTTGATTTAATATAATTG
Found at i:56108 original size:29 final size:30
Alignment explanation
Indices: 56066--56133 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
56056 TATGATTGAA
*
56066 TATACAATTGTATATATG-AATTTTGATTT
1 TATACAATTGTATACATGAAATTTTGATTT
* *
56095 TATATAATTTTATACATGAAATTTTGATTT
1 TATACAATTGTATACATGAAATTTTGATTT
* *
56125 GATCCAATT
1 TATACAATT
56134 CTTGTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (30 bp):
TATACAATTGTATACATGAAATTTTGATTT
Found at i:56729 original size:32 final size:30
Alignment explanation
Indices: 56657--56731 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
56647 TAAATACCTC
* * *
56657 AAAAATTAATA-TAAAACAAACATTTATAT
1 AAAAATTTATATTTAAACAAACATTTAAAT
*
56686 AAATA-TTATATTTAAACAAATCACTTTAAAT
1 AAAAATTTATATTTAAACAAA-CA-TTTAAAT
56717 AAAAATTTATATTTA
1 AAAAATTTATATTTA
56732 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 4 0.11
29 12 0.32
30 2 0.05
31 10 0.27
32 9 0.24
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAAATTTATATTTAAACAAACATTTAAAT
Found at i:68413 original size:11 final size:11
Alignment explanation
Indices: 68397--68441 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
68387 ACCGGGTTCC
68397 TTTTAAATTTA
1 TTTTAAATTTA
68408 TTTTAAATTTGA
1 TTTTAAATTT-A
*
68420 ATTTAAATTTA
1 TTTTAAATTTA
68431 TTTTAAATTTA
1 TTTTAAATTTA
68442 AATTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:68422 original size:6 final size:6
Alignment explanation
Indices: 68398--68447 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
68388 CCGGGTTCCT
* * *
68398 TTTAAA TTT-AT TTTAAA TTTGAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
68444 TTTA
1 TTTA
68448 TTTTCAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:68425 original size:23 final size:23
Alignment explanation
Indices: 68398--68447 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
68388 CCGGGTTCCT
*
68398 TTTAAATTTATTTTAAATTTGAA
1 TTTAAATTTATTTTAAATTTAAA
68421 TTTAAATTTATTTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
68444 TTTA
1 TTTA
68448 TTTTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:68460 original size:17 final size:17
Alignment explanation
Indices: 68397--68457 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
68387 ACCGGGTTCC
*
68397 TTTTAAATTT-ATTTTAA
1 TTTTAAATTTAAATTT-A
* *
68414 ATTTGAATTTAAATTTA
1 TTTTAAATTTAAATTTA
68431 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
68448 TTTTCAAATT
1 TTTT-AAATT
68458 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 28 0.76
18 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:69807 original size:198 final size:197
Alignment explanation
Indices: 69463--69859 Score: 742
Period size: 198 Copynumber: 2.0 Consensus size: 197
69453 AAAAGCGGGA
*
69463 GAAAAGATTTTTTTTTTTTAAAAACGAAACGGTCTTTAGAGAAAGAAAAGAAATGTTTTTTACCT
1 GAAAATATTTTTTTTTTTTAAAAACGAAACGGTCTTTAGAGAAAGAAAAGAAATGTTTTTTACCT
*
69528 CCGGCGGCCCCGACGACGGTGCGTGTGCCTGAGACGATGCATGGATGATGAACAGGGAGGTGTAC
66 CCGGCGACCCCGACGACGGTGCGTGTGCCTGAGACGATGCATGGATGATGAACAGGGAGGTGTAC
69593 CTGACGACCGACGACGATGGGAGGCGACACGGCGCGAGCGTGATGCCTTACGCGCGGGACAAGCA
131 CTGACGACCGACGACGATGGGAGGCGACACGGCGCGAGCGTGATGCCTTACGCGCGGGACAAGCA
69658 CC
196 CC
69660 GANAAATATTTTTTTTTTTTAAAAACGAAACGGTCTTTAGAGAAAGAAAAGAAATGTTTTTTACC
1 GA-AAATATTTTTTTTTTTTAAAAACGAAACGGTCTTTAGAGAAAGAAAAGAAATGTTTTTTACC
69725 TCCGGCGACCCCGACGACGGTGCGTGTGCCTGAGAC-AGTGCATGGATGATGAACAGGGAGGTGT
65 TCCGGCGACCCCGACGACGGTGCGTGTGCCTGAGACGA-TGCATGGATGATGAACAGGGAGGTGT
*
69789 ACCTGACGACCGACGACGATGGGAGGCGGCACGGCGCGAGCGTGATGCCTTACGCGCGGGACAAG
129 ACCTGACGACCGACGACGATGGGAGGCGACACGGCGCGAGCGTGATGCCTTACGCGCGGGACAAG
69854 CACC
194 CACC
69858 GA
1 GA
69860 CGGTCGGNNN
Statistics
Matches: 195, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
197 3 0.02
198 192 0.98
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.20
Consensus pattern (197 bp):
GAAAATATTTTTTTTTTTTAAAAACGAAACGGTCTTTAGAGAAAGAAAAGAAATGTTTTTTACCT
CCGGCGACCCCGACGACGGTGCGTGTGCCTGAGACGATGCATGGATGATGAACAGGGAGGTGTAC
CTGACGACCGACGACGATGGGAGGCGACACGGCGCGAGCGTGATGCCTTACGCGCGGGACAAGCA
CC
Found at i:70432 original size:30 final size:29
Alignment explanation
Indices: 70387--70528 Score: 89
Period size: 29 Copynumber: 4.8 Consensus size: 29
70377 GAAGGTCCCT
*
70387 AAACTATCAAAAAATTCAATTTTTAACCCCA
1 AAACTTTC-AAAAATTCAATTTTT-ACCCCA
70418 AAACTTTCAAAAATT-ATATTTTTA-CCCA
1 AAACTTTCAAAAATTCA-ATTTTTACCCCA
* * *
70446 CGAA-TTTCCAAAAATTTC-ATTTTTGACCTCG
1 -AAACTTT-CAAAAA-TTCAATTTTT-ACCCCA
*
70477 AAACATTCAAAAATT-ACATTTTTACCCTC-
1 AAACTTTCAAAAATTCA-ATTTTTACCC-CA
* * *
70506 GAACTTCCAAAAATTCCATTTTT
1 AAACTTTCAAAAATTCAATTTTT
70529 TACTTTGAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
28 7 0.08
29 39 0.44
30 31 0.35
31 11 0.12
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTTCAAAAATTCAATTTTTACCCCA
Found at i:70487 original size:59 final size:56
Alignment explanation
Indices: 70394--70647 Score: 224
Period size: 59 Copynumber: 4.3 Consensus size: 56
70384 CCTAAACTAT
* * * * *
70394 CAAAAAATTCAATTTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCACGAATTTC
1 CAAAAATTTC-ATTTTTTACCCCGAAAC-TTCAAAAATTACA-TTTTACCC-CGAACTTC
* *
70454 CAAAAATTTCATTTTTGACCTCGAAACATTCAAAAATTACATTTTTACCCTCGAACTTC
1 CAAAAATTTCATTTTTTACCCCGAAAC-TTCAAAAATTACA-TTTTACCC-CGAACTTC
* *** * *
70513 CAAAAATTCCATTTTTTACTTTGAAACTTCTAAAAATTACATTTTACCCCCAAACCTC
1 CAAAAATTTCATTTTTTACCCCGAAACTTC-AAAAATTACATTTTA-CCCCGAACTTC
* * *
70571 CAAACACTCCATTTTTTACCCCGAAACTCTCAAAAATTACCATTTTACCCCTGAA-TGTC
1 CAAAAATTTCATTTTTTACCCCGAAACT-TCAAAAATTA-CATTTTACCCC-GAACT-TC
70630 CAAAAA-TTCTATTTTTTA
1 CAAAAATTTC-ATTTTTTA
70648 TCCTGATTTT
Statistics
Matches: 164, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
58 51 0.31
59 104 0.63
60 9 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (56 bp):
CAAAAATTTCATTTTTTACCCCGAAACTTCAAAAATTACATTTTACCCCGAACTTC
Found at i:70516 original size:29 final size:29
Alignment explanation
Indices: 70419--70645 Score: 141
Period size: 29 Copynumber: 7.8 Consensus size: 29
70409 TTAACCCCAA
* * *
70419 AACTTTCAAAAATTATATTTTTACCCACG
1 AACTTCCAAAAATTACATTTTTACCCTCG
* *
70448 AATTTCCAAAAATTTCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
70477 AAACATT-CAAAAATTACATTTTTACCCTCG
1 -AAC-TTCCAAAAATTACATTTTTACCCTCG
* * *
70507 AACTTCCAAAAATTCCATTTTTTA-CTTTG
1 AACTTCCAAAAATTACA-TTTTTACCCTCG
* * *
70536 AAACTTCTAAAAATTACA-TTTTACCCCCA
1 -AACTTCCAAAAATTACATTTTTACCCTCG
* * * *
70565 AACCTCCAAACACTCCATTTTTTACCC-CG
1 AACTTCCAAAAATTACA-TTTTTACCCTCG
70594 AAAC-TCTCAAAAATTACCA-TTTTACCC-CTG
1 -AACTTC-CAAAAATTA-CATTTTTACCCTC-G
70624 AA-TGTCCAAAAATT-CTATTTTT
1 AACT-TCCAAAAATTAC-ATTTTT
70646 TATCCTGATT
Statistics
Matches: 155, Mismatches: 25, Indels: 36
0.72 0.12 0.17
Matches are distributed among these distances:
27 1 0.01
28 20 0.13
29 66 0.43
30 64 0.41
31 4 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:70529 original size:30 final size:29
Alignment explanation
Indices: 70396--70647 Score: 146
Period size: 30 Copynumber: 8.6 Consensus size: 29
70386 TAAACTATCA
* * * *
70396 AAAAATTCAATTTTTAACCCCAAAACTTTC
1 AAAAATTCCATTTTTTACCCC-GAACTTCC
*
70426 AAAAATT--ATATTTTTACCCACGAATTTCC
1 AAAAATTCCAT-TTTTTACCC-CGAACTTCC
* * *
70455 AAAAATTTCATTTTTGACCTCGAAACATT-C
1 AAAAATTCCATTTTTTACCCCG-AAC-TTCC
*
70485 AAAAATTACA-TTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTTACCC-CGAACTTCC
*** *
70514 AAAAATTCCATTTTTTACTTTGAAACTTCT
1 AAAAATTCCATTTTTTACCCCG-AACTTCC
* * *
70544 AAAAATTACA--TTTTACCCCCAAACCTCC
1 AAAAATTCCATTTTTTA-CCCCGAACTTCC
* *
70572 AAACACTCCATTTTTTACCCCGAAAC-TCTC
1 AAAAATTCCATTTTTTACCCCG-AACTTC-C
70602 AAAAATTACCA--TTTTACCCCTGAA-TGTCC
1 AAAAATT-CCATTTTTTACCCC-GAACT-TCC
*
70631 AAAAATTCTATTTTTTA
1 AAAAATTCCATTTTTTA
70648 TCCTGATTTT
Statistics
Matches: 172, Mismatches: 29, Indels: 42
0.71 0.12 0.17
Matches are distributed among these distances:
28 23 0.13
29 69 0.40
30 73 0.42
31 7 0.04
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTTACCCCGAACTTCC
Found at i:70664 original size:117 final size:118
Alignment explanation
Indices: 70463--70679 Score: 266
Period size: 117 Copynumber: 1.8 Consensus size: 118
70453 CCAAAAATTT
*
70463 CATTTTTGACCTCGAAACATTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTT
1 CATTTTTGACCCCGAAACATTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTT
*
70528 TTACTTTGAAACTTCTAAAAATTAC-ATTTTACCCCCAAACCTCCAAACACTC
66 TTACTCTGAAACTTCTAAAAATTACTATTTTACCCCCAAACCTCCAAACACTC
* *
70580 CATTTTTTACCCCGAAAC-TCTCAAAAATTACCA-TTTTACCC-CTGAA-TGTCCAAAAATTCTA
1 CATTTTTGACCCCGAAACAT-TCAAAAATTA-CATTTTTACCCTC-GAACT-TCCAAAAATTCCA
*** * *
70641 TTTTTTA-TCCTGATTTTTTTAAAAATTACTGTTTTACCC
62 TTTTTTACT-CTGAAACTTCTAAAAATTACTATTTTACCC
70680 TTGGATGTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
116 4 0.05
117 71 0.84
118 10 0.12
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (118 bp):
CATTTTTGACCCCGAAACATTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTT
TTACTCTGAAACTTCTAAAAATTACTATTTTACCCCCAAACCTCCAAACACTC
Found at i:70751 original size:28 final size:28
Alignment explanation
Indices: 70718--70779 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
70708 CAAAATTTTC
* * *
70718 CCAAAATTATCATTTTTCCCTCGAGAAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
*
70746 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
*
70774 TCAAAA
1 CCAAAA
70780 AATCTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGAAT
Found at i:71720 original size:19 final size:19
Alignment explanation
Indices: 71673--71729 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 19
71663 TGTCACGTCA
71673 ATAAATTA-TTTTAAAATT
1 ATAAATTATTTTTAAAATT
71691 ATTAAAATTATTTTTAAAA-T
1 A-T-AAATTATTTTTAAAATT
*
71711 ATAAA-T-TTATTAAAATT
1 ATAAATTATTTTTAAAATT
71728 AT
1 AT
71730 TTTTTTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 8 0.24
17 4 0.12
18 4 0.12
19 2 0.06
20 8 0.24
21 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAATTATTTTTAAAATT
Found at i:71752 original size:31 final size:28
Alignment explanation
Indices: 71684--71773 Score: 110
Period size: 28 Copynumber: 3.1 Consensus size: 28
71674 TAAATTATTT
71684 TAAAATTATTAAAATTATTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
* *
71712 TAAATTTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTA--TTTTTAAAAT-A
* *
71743 TAAAATTATT-AAATAATTATTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
71770 TAAA
1 TAAA
71774 GATTTCATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.09
28 24 0.45
30 14 0.26
31 10 0.19
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:77629 original size:3 final size:3
Alignment explanation
Indices: 77623--77651 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
77613 GGTGGTGATT
77623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
77652 GTCAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:96634 original size:21 final size:21
Alignment explanation
Indices: 96592--96639 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
96582 ATGTGACACA
**
96592 CACGTGATAGACCCTTACAAG
1 CACGTGATAGACCCCAACAAG
* *
96613 CACGTGATAGGCCCCAAGAAG
1 CACGTGATAGACCCCAACAAG
96634 CACGTG
1 CACGTG
96640 CACCCCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (21 bp):
CACGTGATAGACCCCAACAAG
Found at i:99566 original size:31 final size:31
Alignment explanation
Indices: 99531--99595 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
99521 TACAAAATAA
99531 TCACTAAACTATTCAAAAGTTTTCATTTAAG
1 TCACTAAACTATTCAAAAGTTTTCATTTAAG
*** * * *
99562 TCACTAGGTTGTTCGAAAGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAGTTTTCATTTAAG
99593 TCA
1 TCA
99596 ATGGGATGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTTTCATTTAAG
Found at i:102247 original size:31 final size:30
Alignment explanation
Indices: 102212--102276 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
102202 CATTTTGGCT
*
102212 ATTGAACTATTCGAAAGTTTTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAG-C
* *
102243 ATTGAACTATTTAAAAGTTTTTATTTAAGC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGC
102273 ATTG
1 ATTG
102277 GATTGTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (30 bp):
ATTGAACTATTCAAAAGTTTTCATTTAAGC
Found at i:102696 original size:2 final size:2
Alignment explanation
Indices: 102689--102742 Score: 92
Period size: 2 Copynumber: 27.0 Consensus size: 2
102679 GCAGTTTACC
102689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102731 TA T- TA TCA TA TA
1 TA TA TA T-A TA TA
102743 ACCATACGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104834 original size:38 final size:38
Alignment explanation
Indices: 104783--104857 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
104773 GTTAACAGAT
104783 GAGTCCATTGAAGAGTCTGATGAAAAGAATATCATAAC
1 GAGTCCATTGAAGAGTCTGATGAAAAGAATATCATAAC
104821 GAGTCCATTGAAGAGTCTGATGAAAAGAATATCATAA
1 GAGTCCATTGAAGAGTCTGATGAAAAGAATATCATAA
104858 GTCATACATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (38 bp):
GAGTCCATTGAAGAGTCTGATGAAAAGAATATCATAAC
Found at i:121739 original size:15 final size:17
Alignment explanation
Indices: 121710--121741 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
121700 TTAGTGCAAT
121710 AAAAAATAAATAAATTC
1 AAAAAATAAATAAATTC
121727 AAAAAA-AAA-AAATTC
1 AAAAAATAAATAAATTC
121742 TAAGTGAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAAATAAATAAATTC
Found at i:124268 original size:31 final size:29
Alignment explanation
Indices: 124201--124270 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
124191 GTCTCAAGTT
* * *
124201 ACATTTTAGTCACTTATGTTTGAGATGTT
1 ACATTTTAGTCACTTACGTTTCAGATGTA
*
124230 ACATTTTAGTCACTTACGTTATCATATTGTA
1 ACATTTTAGTCACTTACGTT-TCAGA-TGTA
124261 ACATTTTAGT
1 ACATTTTAGT
124271 TAATGAGTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
30 3 0.09
31 13 0.37
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTACGTTTCAGATGTA
Found at i:126397 original size:2 final size:2
Alignment explanation
Indices: 126390--126414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
126380 AAAAATTTAA
126390 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
126415 GACTGTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:133336 original size:40 final size:40
Alignment explanation
Indices: 133281--133361 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
133271 ACATGTAAGT
133281 ATGAATCCTTATTGCTCTGTATCAACAATAATTTTAGGTC
1 ATGAATCCTTATTGCTCTGTATCAACAATAATTTTAGGTC
133321 ATGAATCCTTATTGCTCTGTATCAACAATAATTTTAGGTC
1 ATGAATCCTTATTGCTCTGTATCAACAATAATTTTAGGTC
133361 A
1 A
133362 GCAAAGTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (40 bp):
ATGAATCCTTATTGCTCTGTATCAACAATAATTTTAGGTC
Found at i:141433 original size:16 final size:17
Alignment explanation
Indices: 141412--141444 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
141402 TAAGAAAAAC
*
141412 AAATCGA-CCGAATCGA
1 AAATCGATCCAAATCGA
141428 AAATCGATCCAAATCGA
1 AAATCGATCCAAATCGA
141445 GGTATTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.15
Consensus pattern (17 bp):
AAATCGATCCAAATCGA
Found at i:148909 original size:14 final size:14
Alignment explanation
Indices: 148890--148920 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
148880 TCTACTACCC
148890 TTTTTTTTTCTATT
1 TTTTTTTTTCTATT
*
148904 TTTTTTTTTCTCTT
1 TTTTTTTTTCTATT
148918 TTT
1 TTT
148921 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTCTATT
Found at i:153130 original size:7 final size:7
Alignment explanation
Indices: 153118--153146 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
153108 TTATAGCAGC
153118 CATAAAA
1 CATAAAA
153125 CATAAAA
1 CATAAAA
153132 CATAAAA
1 CATAAAA
153139 CATAAAA
1 CATAAAA
153146 C
1 C
153147 GAGTAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (7 bp):
CATAAAA
Found at i:153516 original size:16 final size:16
Alignment explanation
Indices: 153480--153519 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
153470 AATAAATAAA
**
153480 AAATATATAAATTTATT
1 AAATAT-TAAATTTAAC
153497 AAATATTAAATTTAAC
1 AAATATTAAATTTAAC
153513 AAATATT
1 AAATATT
153520 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAAATTTAAC
Found at i:167631 original size:11 final size:11
Alignment explanation
Indices: 167615--167674 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
167605 AAAGTATGCC
167615 TTAATCTAATA
1 TTAATCTAATA
*
167626 TTAATCTAACA
1 TTAATCTAATA
167637 TTAACATCTAATA
1 TT-A-ATCTAATA
* *
167650 GTAATATAATA
1 TTAATCTAATA
*
167661 TTTATCCTAATA
1 TTAAT-CTAATA
167673 TT
1 TT
167675 GTCATCGACA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 22 0.56
12 9 0.23
13 8 0.21
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAATCTAATA
Found at i:176733 original size:15 final size:15
Alignment explanation
Indices: 176691--176734 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
176681 AAATTTCAAT
176691 AAATAAAAAATTATTA
1 AAATAAAAAA-TATTA
* **
176707 AATTATTAAATATTA
1 AAATAAAAAATATTA
176722 AAATAAAAAATAT
1 AAATAAAAAATAT
176735 AATTATATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:182964 original size:5 final size:5
Alignment explanation
Indices: 182954--182983 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
182944 TTCGCTGGTA
182954 AGCCT AGCCT AGCCT AGCCT AGCCT AGCCT
1 AGCCT AGCCT AGCCT AGCCT AGCCT AGCCT
182984 GAGCTAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
AGCCT
Found at i:184490 original size:15 final size:15
Alignment explanation
Indices: 184470--184503 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
184460 TAGTCTAATC
184470 AATCAACATTGAGCA
1 AATCAACATTGAGCA
184485 AATCAACATTGAGCA
1 AATCAACATTGAGCA
184500 AATC
1 AATC
184504 CATTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (15 bp):
AATCAACATTGAGCA
Found at i:194492 original size:48 final size:48
Alignment explanation
Indices: 194436--194531 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
194426 AAAACCAGAG
194436 TTAATATTATTTCAGCCCTGTTTGTGGCTTAAGGCAATCACACAACAA
1 TTAATATTATTTCAGCCCTGTTTGTGGCTTAAGGCAATCACACAACAA
194484 TTAATATTATTTCAGCCCTGTTTGTGGCTTAAGGCAATCACACAACAA
1 TTAATATTATTTCAGCCCTGTTTGTGGCTTAAGGCAATCACACAACAA
194532 AGACATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (48 bp):
TTAATATTATTTCAGCCCTGTTTGTGGCTTAAGGCAATCACACAACAA
Found at i:212593 original size:45 final size:45
Alignment explanation
Indices: 212528--212617 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
212518 CTAGAATTTA
*
212528 TTACGACACTTGAGTAAAAATAATGAGATCCCCTGGTTAGTTTGT
1 TTACGACACTTAAGTAAAAATAATGAGATCCCCTGGTTAGTTTGT
* *
212573 TTACGGCACTTAAGTCAAAATAATGAGATCCCCTGGTTAGTTTGT
1 TTACGACACTTAAGTAAAAATAATGAGATCCCCTGGTTAGTTTGT
212618 GGGGACTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (45 bp):
TTACGACACTTAAGTAAAAATAATGAGATCCCCTGGTTAGTTTGT
Found at i:222738 original size:72 final size:74
Alignment explanation
Indices: 222621--222768 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 74
222611 TCACCAAGAG
* * *
222621 TATATTTGAGTCTTATTGAATAATGATATTCAACAACGAAGAATAAT-G-ATACTCTCATTAGAG
1 TATATTTGAGCCTTATTGAAGAATGATATTCAACAACGAAGAATAATGGTAGACTCTCATTAGAG
222684 TCTTGTAAT
66 TCTTGTAAT
* *
222693 TATATTTGAGCCTTATTGAAGAATGATATTCAACAACGAGGAATAATGGTAGACTTTCATTAGAG
1 TATATTTGAGCCTTATTGAAGAATGATATTCAACAACGAAGAATAATGGTAGACTCTCATTAGAG
222758 TCTTGTAAT
66 TCTTGTAAT
222767 TA
1 TA
222769 AAAGTTTTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
72 44 0.64
73 1 0.01
74 24 0.35
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (74 bp):
TATATTTGAGCCTTATTGAAGAATGATATTCAACAACGAAGAATAATGGTAGACTCTCATTAGAG
TCTTGTAAT
Found at i:233616 original size:18 final size:18
Alignment explanation
Indices: 233585--233622 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
233575 TCACGATTCT
233585 TTTTTACTAAATTATAATA
1 TTTTTACTAAATTAT-ATA
*
233604 TTTTTA-TATATTATATA
1 TTTTTACTAAATTATATA
233621 TT
1 TT
233623 GAAATGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTACTAAATTATATA
Found at i:240124 original size:17 final size:18
Alignment explanation
Indices: 240104--240137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
240094 AAAATTAATG
240104 TAAAAA-AAAAAATTGAA
1 TAAAAATAAAAAATTGAA
*
240121 TAAAAATGAAAAATTGA
1 TAAAAATAAAAAATTGA
240138 TGCATATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
TAAAAATAAAAAATTGAA
Found at i:240427 original size:18 final size:18
Alignment explanation
Indices: 240404--240440 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
240394 TTTGTTATCA
240404 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
240422 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
240440 A
1 A
240441 CATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:242869 original size:22 final size:21
Alignment explanation
Indices: 242822--242869 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
242812 GACTTTCTTG
*
242822 ATTAACTTAATTAATCATTTT
1 ATTAACTTAATTAATCATATT
* *
242843 TTTAACCTTAATTAATCCTATT
1 ATTAA-CTTAATTAATCATATT
242865 ATTAA
1 ATTAA
242870 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:244534 original size:28 final size:28
Alignment explanation
Indices: 244479--244542 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
244469 CCTAACGGAG
* * *
244479 TTCCACATATAAGATAATCCTAGCAGAC
1 TTCCACATATAAGACAATACTAGAAGAC
* *
244507 TTCTACATATAAGACAATACTGGAAGAC
1 TTCCACATATAAGACAATACTAGAAGAC
244535 TTCCACAT
1 TTCCACAT
244543 CTTTCATAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (28 bp):
TTCCACATATAAGACAATACTAGAAGAC
Found at i:246037 original size:16 final size:16
Alignment explanation
Indices: 246016--246048 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
246006 TGATGATTTT
*
246016 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
246032 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
246048 A
1 A
246049 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:246486 original size:18 final size:16
Alignment explanation
Indices: 246463--246498 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
246453 CTTAGTAAAT
246463 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
246481 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
246497 AT
1 AT
246499 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:247116 original size:52 final size:52
Alignment explanation
Indices: 247039--247329 Score: 465
Period size: 52 Copynumber: 5.6 Consensus size: 52
247029 TAAATGCAAA
* ** *
247039 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAAATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
247091 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
247143 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
247195 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTAACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
247247 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTCGGATTTTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
247299 AGGTCCGATGACTATGTCTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
247330 TAAATGAGAA
Statistics
Matches: 222, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 222 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:247452 original size:62 final size:62
Alignment explanation
Indices: 247299--247452 Score: 247
Period size: 62 Copynumber: 2.5 Consensus size: 62
247289 TCGGATTTTG
* *
247299 AGGTCCGATGACTATGTCTCATCGTGAGTATTAAATGAGAAATGAATCTTATTACAGATTAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTTTTAAATGAGAAATGAATCTTATTACAGATTAA
* * *
247361 AGGTCCGATAACTATGTGCCATCGTGAGTTTTAAATGAGAAATGAATCTTATTACGGATTAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTTTTAAATGAGAAATGAATCTTATTACAGATTAA
247423 AGGTCCGATGACT-TCGTGTCATCGTGAGTT
1 AGGTCCGATGACTAT-GTGTCATCGTGAGTT
247453 ACCGAATGCG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
61 1 0.01
62 83 0.99
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (62 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTTTTAAATGAGAAATGAATCTTATTACAGATTAA
Found at i:250955 original size:52 final size:52
Alignment explanation
Indices: 250877--251023 Score: 222
Period size: 52 Copynumber: 2.8 Consensus size: 52
250867 AAATGAAAAA
250877 AAGGTCCGATGACTAAGTGTTATCGTGAGTACATGAATCCTTCACGGATTAT
1 AAGGTCCGATGACTAAGTGTTATCGTGAGTACATGAATCCTTCACGGATTAT
* * *
250929 AAGGTCCAATGACTAAGTGTCATCGTGAGTACAAGAATCCTTCACGGATTAT
1 AAGGTCCGATGACTAAGTGTTATCGTGAGTACATGAATCCTTCACGGATTAT
* * * *
250981 AAGGTCTGATAACTAAGTGTTATCGTGGGTATATGAATTCCTT
1 AAGGTCCGATGACTAAGTGTTATCGTGAGTACATGAA-TCCTT
251024 TATGGAACAA
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 79 0.94
53 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (52 bp):
AAGGTCCGATGACTAAGTGTTATCGTGAGTACATGAATCCTTCACGGATTAT
Found at i:251711 original size:21 final size:21
Alignment explanation
Indices: 251645--251711 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
251635 CACTGACTTG
*
251645 AGATGTATCGGTAG-TTGAAT
1 AGATGTATCGGTAGTTTGCAT
*
251665 TG-TGAGTATCGGTAGTTTTATGCAT
1 AGAT--GTATCGGTAG--TT-TGCAT
251690 AGATGTATCGGTAGTTTGCAT
1 AGATGTATCGGTAGTTTGCAT
251711 A
1 A
251712 CTTGTACCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 16 0.43
22 2 0.05
24 11 0.30
25 5 0.14
26 1 0.03
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.39
Consensus pattern (21 bp):
AGATGTATCGGTAGTTTGCAT
Found at i:251717 original size:21 final size:23
Alignment explanation
Indices: 251670--251724 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
251660 TGAATTGTGA
*
251670 GTATCGGTAGTTTTATGCATAGAT
1 GTATCGGTAG-TTTATGCATACAT
*
251694 GTATCGGTAG-TT-TGCATACTT
1 GTATCGGTAGTTTATGCATACAT
*
251715 GTACCGGTAG
1 GTATCGGTAG
251725 AAGTTATAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.57
22 2 0.07
24 10 0.36
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (23 bp):
GTATCGGTAGTTTATGCATACAT
Found at i:252111 original size:17 final size:17
Alignment explanation
Indices: 252086--252145 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
252076 TGATTTTAAA
*
252086 TTAAGTTTAAATTGGTT
1 TTAAATTTAAATTGGTT
*
252103 TTAAATTTAAATT--TAA
1 TTAAATTTAAATTGGT-T
252119 TTAAATTTGAAA-TGGTT
1 TTAAATTT-AAATTGGTT
*
252136 TTAAACTTAA
1 TTAAATTTAA
252146 TATTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 1 0.03
16 11 0.31
17 22 0.63
18 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (17 bp):
TTAAATTTAAATTGGTT
Found at i:252135 original size:33 final size:34
Alignment explanation
Indices: 252081--252157 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
252071 ACTTTTGATT
* *
252081 TTAAATTAAGTTTAAATTGGTTTTAAATTTAA-A
1 TTAAATTAAATTTAAATTGGTTTTAAACTTAATA
*
252114 TTTAATTAAATTTGAAA-TGGTTTTAAACTTAATA
1 TTAAATTAAATTT-AAATTGGTTTTAAACTTAATA
252148 TTAAATTAAA
1 TTAAATTAAA
252158 AAGCCCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (34 bp):
TTAAATTAAATTTAAATTGGTTTTAAACTTAATA
Found at i:253931 original size:40 final size:40
Alignment explanation
Indices: 253876--253952 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
253866 ACGTGTCCTA
253876 TATTTGGCTTATTTATGCAATTGATCCTTCCCCTTTTTAC
1 TATTTGGCTTATTTATGCAATTGATCCTTCCCCTTTTTAC
253916 TATTTGGCTTATTTATGCAATTGATCCTTCCCCTTTT
1 TATTTGGCTTATTTATGCAATTGATCCTTCCCCTTTT
253953 ACTTTCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.17, C:0.22, G:0.10, T:0.51
Consensus pattern (40 bp):
TATTTGGCTTATTTATGCAATTGATCCTTCCCCTTTTTAC
Found at i:254210 original size:57 final size:57
Alignment explanation
Indices: 254141--254326 Score: 182
Period size: 57 Copynumber: 3.2 Consensus size: 57
254131 GAAGTTTTCA
* * *
254141 AAAATTGCA-TTTTGACCCTCAAACTTCCCAAAAATTACATTTTTACCCT-TACCTTCC
1 AAAATTACATTTTTGACCCTCAAA-TTTCCAAAAATTACA-TTTTACCCTCAACCTTCC
** * * *
254198 AAAATTACATTTTTTTCCC-CGATTTTCCAAAAATTACATTTTACCCTCGAACTTTCC
1 AAAATTACATTTTTGACCCTCAAATTTCCAAAAATTACATTTTACCCTC-AACCTTCC
* * * *
254255 AAAATTCCATTTTTGACCCT-AAATTTTCAAAAAATACATTTTACCCCCAAACCTTCC
1 AAAATTACATTTTTGACCCTCAAATTTCCAAAAATTACATTTTACCCTC-AACCTTCC
254312 AAAAATTACCATTTT
1 -AAAATTA-CATTTT
254327 ACCCCCAATG
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
55 9 0.09
56 14 0.13
57 62 0.60
58 13 0.12
59 6 0.06
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (57 bp):
AAAATTACATTTTTGACCCTCAAATTTCCAAAAATTACATTTTACCCTCAACCTTCC
Found at i:254316 original size:28 final size:29
Alignment explanation
Indices: 254139--254387 Score: 151
Period size: 29 Copynumber: 8.7 Consensus size: 29
254129 CTGAAGTTTT
* * *
254139 CAAAAATTGCATTTTGACCCTCAAACTTCC
1 CAAAAATTACATTTT-ACCCCCAAACTTTC
** *
254169 CAAAAATTACATTTTTA--CCCTTACCTTC
1 CAAAAATTACA-TTTTACCCCCAAACTTTC
** * *
254197 C-AAAATTACATTTTTTTCCCC-GATTTTC
1 CAAAAATTACA-TTTTACCCCCAAACTTTC
* *
254225 CAAAAATTACATTTTACCCTCGAACTTTC
1 CAAAAATTACATTTTACCCCCAAACTTTC
* * *
254254 C-AAAATTCCATTTTTGA-CCCTAAA-TTTT
1 CAAAAATTACA-TTTT-ACCCCCAAACTTTC
* *
254282 CAAAAAATACATTTTACCCCCAAACCTTC
1 CAAAAATTACATTTTACCCCCAAACTTTC
*
254311 CAAAAATTACCATTTTACCCCC-AA-TGTC
1 CAAAAATTA-CATTTTACCCCCAAACTTTC
* * *
254339 CAAAAA-TACCATTTCGACCCCGAATCTTT-
1 CAAAAATTA-CATTT-TACCCCCAAACTTTC
254368 CAAAAATTACCATTTTACCC
1 CAAAAATTA-CATTTTACCC
254388 ATGGATGTCT
Statistics
Matches: 171, Mismatches: 33, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
27 23 0.13
28 54 0.32
29 56 0.33
30 34 0.20
31 4 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTACCCCCAAACTTTC
Found at i:254343 original size:57 final size:57
Alignment explanation
Indices: 254223--254442 Score: 187
Period size: 57 Copynumber: 3.8 Consensus size: 57
254213 TCCCCGATTT
* * * *
254223 TCCAAAAATTACATTTTACCCTCGAACTTTCC-AAAATT-CCATTTTTGACCCTAAATT
1 TCCAAAAAATACATTTTACCCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCTAAATG
* * **
254280 TTCAAAAAATACATTTTACCCCCAAACCTTCCAAAAATTACCATTTTACCCCCAATG
1 TCCAAAAAATACATTTTACCCCCGAACCTTCCAAAAATTACCATTTTACCCTAAATG
* * * **
254337 TCC-AAAAATACCATTTCGA-CCCCGAATCTTTCAAAAATTACCATTTTACCCATGGATG
1 TCCAAAAAATA-CATTT-TACCCCCGAACCTTCCAAAAATTACCATTTTACCC-TAAATG
* * * * * *
254395 TCTAAAAATTCCATTTTTAACCTCGAACCTTCCGAAAATTACCATTTT
1 TCCAAAAAATACA-TTTTACCCCCGAACCTTCCAAAAATTACCATTTT
254443 GTTCCTGAAG
Statistics
Matches: 131, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
56 7 0.05
57 70 0.53
58 19 0.15
59 35 0.27
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (57 bp):
TCCAAAAAATACATTTTACCCCCGAACCTTCCAAAAATTACCATTTTACCCTAAATG
Found at i:256399 original size:8 final size:8
Alignment explanation
Indices: 256386--256415 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
256376 ATAAATTTTG
256386 AATTTTAA
1 AATTTTAA
256394 AATTTTAA
1 AATTTTAA
256402 AATTTTAA
1 AATTTTAA
256410 AATTTT
1 AATTTT
256416 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AATTTTAA
Found at i:256898 original size:14 final size:16
Alignment explanation
Indices: 256879--256910 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
256869 CTTCATCTTC
256879 TTTCTTTT-A-ATTTT
1 TTTCTTTTGAGATTTT
256893 TTTCTTTTGAGATTTT
1 TTTCTTTTGAGATTTT
256909 TT
1 TT
256911 GATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTCTTTTGAGATTTT
Found at i:264724 original size:14 final size:15
Alignment explanation
Indices: 264663--264728 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
264653 GGTTTTTTAT
*
264663 AAAAAT-ATTATTA-
1 AAAAATAATAATTAC
*
264676 AAAATTAATTAATTAC
1 AAAAATAA-TAATTAC
* *
264692 AAAAATAA-AATGAT
1 AAAAATAATAATTAC
*
264706 AAAAAAAATAATTAC
1 AAAAATAATAATTAC
264721 AAAAATAA
1 AAAAATAA
264729 AATATTTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
13 5 0.12
14 12 0.30
15 16 0.40
16 7 0.17
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATAATAATTAC
Found at i:264730 original size:17 final size:17
Alignment explanation
Indices: 264675--264732 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
264665 AAATATTATT
* *
264675 AAAAATTAATTAATTAC
1 AAAAATAAAATAATTAC
*
264692 AAAAATAAAATGA-T--
1 AAAAATAAAATAATTAC
264706 -AAAA-AAAATAATTAC
1 AAAAATAAAATAATTAC
264721 AAAAATAAAATA
1 AAAAATAAAATA
264733 TTTGTTGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
16 5 0.16
17 16 0.50
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATAAAATAATTAC
Found at i:265005 original size:15 final size:14
Alignment explanation
Indices: 264975--265007 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
264965 TTTTTTTTCA
*
264975 TTTATTCAGATTTT
1 TTTAATCAGATTTT
264989 TTTAATCAGATTTT
1 TTTAATCAGATTTT
265003 TTTAA
1 TTTAA
265008 AATTTACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TTTAATCAGATTTT
Found at i:269716 original size:25 final size:25
Alignment explanation
Indices: 269666--269724 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
269656 TAAGATAATT
*
269666 ATATAAAAAATTTTAATAAATAAAA
1 ATATATAAAATTTTAATAAATAAAA
* *
269691 ATATATAAAATTATTAA-ATATTAAA
1 ATATATAAAATT-TTAATAAATAAAA
269716 ATAATATAA
1 AT-ATATAA
269725 TATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATATAAAATTTTAATAAATAAAA
Found at i:272650 original size:43 final size:44
Alignment explanation
Indices: 272573--272658 Score: 99
Period size: 45 Copynumber: 2.0 Consensus size: 44
272563 AATATTTTTA
272573 TTTAATTTAGAATTTTTTTTAAAGCAGAGAAAATTGAT-TTTGAG
1 TTTAATTTAGAATTTTTTTTAAAGCAGAGAAAATT-ATATTTGAG
* *
272617 TTTAATTTATGAGTTTTTTTTCAAG-A-ACG-AAATTATATTTGA
1 TTTAATTTA-GAATTTTTTTTAAAGCAGA-GAAAATTATATTTGA
272659 ATAAGGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
42 2 0.05
43 11 0.30
44 11 0.30
45 13 0.35
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (44 bp):
TTTAATTTAGAATTTTTTTTAAAGCAGAGAAAATTATATTTGAG
Found at i:275011 original size:12 final size:12
Alignment explanation
Indices: 274996--275027 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
274986 TAAAAAGGTA
274996 AAAGAAAATGAC
1 AAAGAAAATGAC
275008 AAAGAAAATGAC
1 AAAGAAAATGAC
275020 AAAGAAAA
1 AAAGAAAA
275028 AGAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.72, C:0.06, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAGAAAATGAC
Found at i:278413 original size:41 final size:41
Alignment explanation
Indices: 278359--278473 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 41
278349 TTTGGACATA
278359 AAACGCCGCAAAAGGTAAAAGCAATAGCGGCGTTTCTGCAT
1 AAACGCCGCAAAAGGTAAAAGCAATAGCGGCGTTTCTGCAT
*
278400 AAACGCCGCAAAAGGT-AAAGCAATAGCGGTGTTTCTGCAT
1 AAACGCCGCAAAAGGTAAAAGCAATAGCGGCGTTTCTGCAT
* *
278440 AAATGCTGCAAAAGGTAAAA-CAATAGCGGCGTTT
1 AAACGCCGCAAAAGGTAAAAGCAATAGCGGCGTTT
278474 ATAGAAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
40 50 0.72
41 19 0.28
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.19
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTAAAAGCAATAGCGGCGTTTCTGCAT
Found at i:278568 original size:41 final size:41
Alignment explanation
Indices: 278511--278760 Score: 290
Period size: 41 Copynumber: 6.1 Consensus size: 41
278501 GCATTAACGA
* *
278511 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGTGTCG
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
* **
278552 CTAAAGGTCAGAGCATTAGTAGCGTTTATG-GAAAAGAGCCG
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAG-AAAGAGCCG
* * * * * *
278593 CTAAAGGTCATAGCATTAGAGGCATTTATGGGAAAGTGCCG
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
* * ** *
278634 CTATAGGTTAGAGCATTAGCGGCATTTAT-AGGAAAGCCCCA
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGA-GAAAGAGCCG
* *
278675 CTAAAGGTTAGAGCATTAGCGGGGTTTATG-GAAAGCGCCG
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
*
278715 CTAAAGATTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
1 CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
278756 CTAAA
1 CTAAA
278761 TATCAGAAAT
Statistics
Matches: 178, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 37 0.21
41 140 0.79
42 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAGAGCCG
Found at i:285691 original size:99 final size:99
Alignment explanation
Indices: 285520--285716 Score: 331
Period size: 99 Copynumber: 2.0 Consensus size: 99
285510 ATAGTTATCT
* *
285520 TTGGATTGGTGAATCTTAAACTAACATAGTATTTTAGGCTTTTGTGAAATCGTCCTTTCATTTAT
1 TTGGATTGGTGAAACTTAAACTAACATAGTATTTTAGGCTTTTGTGAAATCATCCTTTCATTTAT
285585 ATAGAGTCAATGTCTCAACAATTTTCTCAAGCTG
66 ATAGAGTCAATGTCTCAACAATTTTCTCAAGCTG
* * **
285619 TTGGATTGGTGAAACTTAATCTTACATAGTATTTTAGGCTTTTGTGAGTTCATCCTTTCATTTAT
1 TTGGATTGGTGAAACTTAAACTAACATAGTATTTTAGGCTTTTGTGAAATCATCCTTTCATTTAT
*
285684 ATAGAGTCGATGTCTCAACAATTTTCTCAAGCT
66 ATAGAGTCAATGTCTCAACAATTTTCTCAAGCT
285717 TTTGAGATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (99 bp):
TTGGATTGGTGAAACTTAAACTAACATAGTATTTTAGGCTTTTGTGAAATCATCCTTTCATTTAT
ATAGAGTCAATGTCTCAACAATTTTCTCAAGCTG
Found at i:293940 original size:29 final size:30
Alignment explanation
Indices: 293888--293966 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
293878 TTTGAATCGT
* * * *
293888 AATTAAAATTTCACGTGTGCAATT-ATATCA
1 AATTAAAA-TTCATGTATACAATTCACATCA
*
293918 AATTAAAATTCATGTATACAATTGCACATTA
1 AATTAAAATTCATGTATACAATT-CACATCA
*
293949 AAATAAAATTCATGTATA
1 AATTAAAATTCATGTATA
293967 ATTTTAAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.29
30 8 0.20
31 21 0.51
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (30 bp):
AATTAAAATTCATGTATACAATTCACATCA
Found at i:295653 original size:17 final size:18
Alignment explanation
Indices: 295631--295669 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
295621 ATATAAAATT
*
295631 AATAAAAAATACGAA-AA
1 AATAAAAAATACCAATAA
295648 AAT-AAAAATACCAATAA
1 AATAAAAAATACCAATAA
295665 AATAA
1 AATAA
295670 TGATTACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 10 0.53
17 8 0.42
18 1 0.05
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (18 bp):
AATAAAAAATACCAATAA
Found at i:301715 original size:10 final size:10
Alignment explanation
Indices: 301702--301730 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
301692 AATTTATTAT
301702 TAGTACGCAA
1 TAGTACGCAA
301712 TAGTACGCAA
1 TAGTACGCAA
301722 TAGTACGCA
1 TAGTACGCA
301731 GGGATATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (10 bp):
TAGTACGCAA
Found at i:310474 original size:5 final size:5
Alignment explanation
Indices: 310464--310499 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
310454 AAGATAACTT
310464 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
310500 AGAAACAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:314360 original size:26 final size:26
Alignment explanation
Indices: 314330--314382 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
314320 GTCTTAAAAT
314330 ATTCTGATGTATCTAATTAAATCTCA
1 ATTCTGATGTATCTAATTAAATCTCA
314356 ATTCTGATGTATCTAATTAAATCTCA
1 ATTCTGATGTATCTAATTAAATCTCA
314382 A
1 A
314383 CTCGATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (26 bp):
ATTCTGATGTATCTAATTAAATCTCA
Found at i:316546 original size:136 final size:135
Alignment explanation
Indices: 316302--316549 Score: 298
Period size: 136 Copynumber: 1.8 Consensus size: 135
316292 TAACTTCCTC
* * * *
316302 CCAGAAAATATAATACTGTCAGCCTCAACGAAGGAACATTTATTCAGATGAACTGCCACTATAGA
1 CCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCCACTAGAGA
* * * * *
316367 ATCCCATCATAAACTAGTAGAACTATCATGTTTAAAATGAACTTTTAAAAAAGTTCAACCAGAAT
66 ATCCCACCACAAACAAGTAGAACTATCAAGTTTAAAATAAACTTTTAAAAAAGTTCAACCAGAAT
316432 TCCCT
131 TCCCT
* * * ** * * * *
316437 CCAGAAAATATAAAATTGTTAGCCCTCAATAAAGGAATGTTTATTTAGGTGGACTCCCACTCGAG
1 CCAGAAAATATAAAACTGTCAG-CCTCAACAAAGGAACATTTATTCAGATGAACTCCCACTAGAG
* * *
316502 AATCCCACCACGAACAAGTAGAATTATCAAGTTTCAAATAAACTTTTA
65 AATCCCACCACAAACAAGTAGAACTATCAAGTTTAAAATAAACTTTTA
316550 GAAATGCTGA
Statistics
Matches: 91, Mismatches: 21, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
135 19 0.21
136 72 0.79
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (135 bp):
CCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCCACTAGAGA
ATCCCACCACAAACAAGTAGAACTATCAAGTTTAAAATAAACTTTTAAAAAAGTTCAACCAGAAT
TCCCT
Found at i:325345 original size:21 final size:21
Alignment explanation
Indices: 325321--325372 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
325311 AAACAAATTA
325321 TAAAAATTATAAGAAATT-AAT
1 TAAAAATTATAA-AAATTAAAT
*
325342 TAAAAATATATAATAATTAAAT
1 TAAAAAT-TATAAAAATTAAAT
325364 TATAAAATT
1 TA-AAAATT
325373 TTATAATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.41
22 11 0.41
23 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAAATTATAAAAATTAAAT
Found at i:325347 original size:22 final size:22
Alignment explanation
Indices: 325315--325372 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
325305 ATTAGGAAAC
325315 AAATTATAAAAATTATAAGAAATT
1 AAATTA-AAAAATTATAA-AAATT
*
325339 -AATT-AAAAATATATAATAATT
1 AAATTAAAAAAT-TATAAAAATT
*
325360 AAATTATAAAATT
1 AAATTAAAAAATT
325373 TTATAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 10 0.34
22 10 0.34
23 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATTAAAAAATTATAAAAATT
Found at i:327008 original size:6 final size:6
Alignment explanation
Indices: 326999--327023 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
326989 ACAACAACAG
326999 CAGCAA CAGCAA CAGCAA CAGCAA C
1 CAGCAA CAGCAA CAGCAA CAGCAA C
327024 GGGAACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:337820 original size:48 final size:49
Alignment explanation
Indices: 337725--337824 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 49
337715 ATTTAATCAC
* *
337725 TTTAATATTAAATTAATATAATACTTATTAAGATAAATATTAGATTAAA
1 TTTAATATTAAATTAATAAAATACTTATTAAGATAAATATTAAATTAAA
*
337774 TTTAATATTAAATTAATAAAATA-TTATTAAGATAATTATTAAATTAAA
1 TTTAATATTAAATTAATAAAATACTTATTAAGATAAATATTAAATTAAA
337822 TTT
1 TTT
337825 TTATAAATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 26 0.54
49 22 0.46
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (49 bp):
TTTAATATTAAATTAATAAAATACTTATTAAGATAAATATTAAATTAAA
Done.